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6,363 results for “Mutations”
YY1 mutations disrupt corticogenesis through a cell type-specific rewiring of cell-autonomous and non-cell-autonomous transcriptional programs
<p>This supplementary data includes counts from bulk and pseudobulk omic experiments, h5ad for single-cell experiments, and outputs of differential expression and enrichments performed on different omics assays.</p>
Mutation Testing in the Wild: Findings from GitHub
<p>Supplementary material for the articule "Mutation Testing in the Wild: Findings from GitHub" submitted to the Empirical Software Engineering Journal. It includes:</p> <ul> <li>Literature_search_for_mutation_tools_2018-2021.xlsx. This document contains the papers found in the search for mutation testing tools performed between 2018 and 2021.</li> <li>Mutation_tools.xlsx: This document includes the 127 mutation testing tools identified in our study along with tables and graphs.</li> <li>Repositories_raw_data.xlsx: All repositories data mined from Github as evidence of use of the top 10 mutation tools analyzed in our study. In addition, tables with calculations and graphs used in our work are included.</li> <li>Search_strings_mutation_tools.xlsx: The search strings used to look for repositories using each mutation tool in Github.</li> </ul>
Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome
<p><br> Abbreviation of species names in each folder: Palb, P. alba; Pade, P. adenopoda; Pdav, P. davidiana; Ptra, P. tremula; Ptrs, P. tremuloides; Prot, P. rotundifolia; Pqio,P. qiongdaoensis.</p> <p>1. FST<br> Relative divergence (FST) for pairwise species comparisons was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>2. dxy<br> Absolute divergence (dxy) was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>3. Nucleotide diversity<br> Nucleotide diversity (π) was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>4. Derived allele frequency<br> The derived frequencies of 4 different functional categories. Each folder contains seven Populus resluts</p> <p>5. Derived_allele_statistics<br> The statistics of homozygous and heterozygous derived alleles for loss of function, deleterious, tolerated and synonymous variants for each individual. The last two individuals in each file are outgroups </p> <p>6. dsuite-dinvestigate<br> The outputs of 10 trios using program Dinvestigate from Dsuite. The sliding window is 50 SNPs, and the step is 20 SNPs.</p> <p>7. Recombination rate<br> The result of population-scaled recombination rate was calculated by LDhat v2.2.</p> <p>8. Volcanofinder<br> Genome-wide scans of introgression sweeps within each species was implemented using VolcanFinder v.1.0 with the Model over 10 Kbp non-overlapping windows.</p> <p>9. ihh12<br> phased SNPs were used to computed ihh12 by selscan v1.3.0. </p> <p>10 populus162.phased.recode.vcf.gz<br> SNPs were phased with Beagle v.4.1 for the 162 non-hybrid individuals.</p> <p>11 populus227.snp.rm_indel.para_filter.biallelic.GQ30.max_miss20.bed.recode.vcf.gz <br> The vcf of 227 Populus samples. </p>
All-atom Molecular Dynamics Simulations of Meiosis 1-associated protein (M1AP) to Investagate the Impact of Known Missense Mutations Associated with Male Infertility through Non-obstructive Azoospermia
<p>Protein structure of meiosis 1-associated protein (M1AP) was modelled by using GalaxyWeb (from Seok Lab). We used this model to investigate the impact of variants (i.e., S50P, R266Q, P389L, G317R, and L430P) in M1AP which were recently associated with non-obstructive azoospermia (NOA). NOA is a male infertility-related condition causing absence of sperm in the seminal fluid due to meiosis failure. We aimed to elucidate the pathogenicity mechanisms of these five missense NOA-related mutations on M1AP by performing molecular modeling and molecular dynamics (MD) simulations. This dataset includes the results of 1000 ns MD simulations (two repeats, each 500 ns) for each of the mutant and wild-type systems.</p> <p>Systems were prepared in Visual Molecular Dynamics (VMD 1.9.3) by placing them in a TIP3P water box with approximately 20 Å thickness from the protein surface and neutralizing the system charge with 0.15 M KCl. Of note, only protein parts were kept for the submission to reduce the size of files. Nanoscale Molecular Dynamics (NAMD 2.13-CUDA) was used to perform MD simulations with CHARMM36m force field. For pressure and temperature controls, Nosé-Hoover Langevin barostat and Langevin thermostat were used. ShakeH algorithm of NAMD was applied for water molecule constraints. 12 Å cut-off distance was used for van der Waals interactions. Switching function starts at 10 Å and reaches zero at 14 Å. Integration time-step was 2 fs. To compute the long-range Coulomb interactions, the particle-mash Ewald method was used. NPT ensemble was applied for whole simulations. Two step minimization & equilibration procedure was performed: (1) 5,000-step minimization and 1 ns equilibrium with constraints on the protein; (2) 5,000-step minimization and 1 ns equilibrium without the constraints on the protein. All related configuration files for wild-type system were also included to the dataset. Production simulations were run twice along 500 ns by using different random seeds to assign the velocities from Boltzmann distribution (total simulation time for each system was 1000 ns, which are given as 500 ns repeat 1, and 500 ns repeat 2). The production simulations were supplied in the dataset. "out" and "log" files were used for energy analysis.</p> <p>For all analysis scripts, see https://github.com/ugerlevik/M1AP_analysis.</p>
Bevacizumab plus erlotinib versus erlotinib alone as first line treatment of patients with EGFR-mutated advanced nonsquamous non-small cell lung cancer. BEVacizumab plus ERLotinib studY (BEVERLY): an academic, multicenter, randomised phase III trial.
<p>Background. Adding bevacizumab to erlotinib prolonged PFS of patients with EGFR-mutated advanced NSCLC in the Japanese NEJ026 trial, but limited data were available in non-Asian patients. BEVERLY is an Italian, multicenter, randomized phase III trial of bevacizumab plus erlotinib versus erlotinib alone as first-line treatment of advanced EGFR-mutated NSCLC.</p> <p>Methods. Eligible patients were randomized 1:1 to erlotinib (150mg daily) plus bevacizumab (15mg/kg iv q3w) or erlotinib alone, until disease progression or unacceptable toxicity. Center, ECOG PS and type of mutation (ex19 deletion vs ex21 L858R vs others) were stratification variables. Investigator-assessed PFS (IA-PFS) and blinded-independent centrally-reviewed PFS (BICR-PFS) were co-primary endpoints. With 80% power in detecting a 0·60 HR and 2–sided α error 0·05, 126 events out of 160 patients were needed. The trial was registered as NCT02633189 and EudraCT 2015-002235-17.</p> <p>Findings. From Apr 11, 2016 to Feb 27, 2019, 160 pts were randomized to erlotinib pus bevacizumab (80) or erlotinib alone (80). Baseline characteristics were balanced between arms; 34 (42·5%) patients in erlotinib plus bevacizumab arm and 43 (53·8%) in erlotinib arm were former or current smokers. At a median follow-up of 36·3 months, 140 PFS events (87·5%) were reported, 68 with erlotinib plus bevacizumab and 72 with erlotinib. Median IA-PFS was 15·4 months (95% CI 12·2–18·6) with erlotinib plus bevacizumab and 9·6 months (95% CI 8·2–10·6) with erlotinib (HR 0·66; 95%CI: 0·47–0·92). BICR-PFS analysis confirmed this result. A significant interaction with treatment effect was found for smoking habit (P=0·0323): former or current smokers receiving erlotinib plus bevacizumab had a longer PFS (16·9 months [95% CI 10·2–21·8] versus 8·8 months [95% CI 5·6–9·6]) than those receiving erlotinib alone.</p> <p>Hypertension (grade≥3: 24% vs 5%), skin rash (grade≥3: 31% vs 14%), thromboembolic events (any grade: 11% vs 4%), and proteinuria (any grade: 23% vs 6%) were more frequent with the combination treatment.</p> <p>Interpretation. The addition of bevacizumab to first-line erlotinib significantly prolonged PFS in Italian patients with EGFR-mutated NSCLC, without unexpected safety issues.</p>
Mutations in the telomerase reverse transcriptase promoter and PIK3CA gene are common events in penile squamous cell carcinoma of Italian and Ugandan patients
<p>Somatic mutations in the promoter region of TERT (TERTp) gene are highly frequent in penile carcinoma in Italian and Ugandan patients, predominantly in human papillomavirus (HPV) negative cancers (67.6%). TERTp and PIK3CA hotspot changes coexist in 15.8% of cases. The higher mutant allele frequencies (MAFs) of TERT -124A/-146A compared to PIK3CA E545K MAFs suggest an asynchronous mutation timing. The coexistence of TERTp and PIK3CA mutations may represent a novel co-actionable therapeutic target in penile carcinoma patients.</p>
In vitro mutation induction: a database of x-ray and particle irradiation experiments
<p>The database presents a collection of <em>in vitro</em> mutation induction data after photon and particle beam irradiation. The experiments included in the database were all performed by means of the <em>hprt</em> mutation assay. The collection was based on extensive literature search, and contains data published in the time period from 1977 to 2002.</p> <p>As better described in the README file, the database provides information on RBE for cell killing and mutation induction, as well as dose response curves raw data for both endpoints, as digitised (when available) from the original publication.</p> <p>This study is part of a manuscript that was submitted for publication in April 2022.</p>
Selpercatinib treatment of RET mutated thyroid cancers is associated with gastrointestinal adverse effects
<p><strong>Background:</strong></p> <p>Metastatic medullary thyroid carcinoma (MTC) and radioactive iodine refractory differentiated thyroid carcinoma (RAI-R DTC) have poor prognosis and limited treatment options. Selpercatinib (LOXO-292), a selective kinase inhibitor targeting the <em>RET</em> gene, has shown a 69-79% objective responses have been observed in this cohort (1) with benefits in other tumours harbouring the same oncogenic driver (2). Published reports describe only 17% of patients experiencing gastrointestinal Adverse effects (AE) which is in contrast to our local experience. Here we characterise the AE and correlate with radiological and histopathological findings. </p> <p><strong>Methods:</strong></p> <p>Sequential patients enrolled in LIBRETTO-001 at Royal North Shore Hospital, Sydney with available imaging (n=22) were recruited. Patients had regular visits with AE documented and CT scans 3 monthly. CT at screening, at time of gastrointestinal AE and at most recent follow up were reviewed and scored. Endoscopic examination was performed in five patients.</p> <p><strong>Results:</strong></p> <p>Of 22 patients in this cohort, the majority had somatic <em>RET </em>alterations (n=18), most commonly <em>p.Met918Thr</em> (n=14). Ten patients (50%) developed gastrointestinal adverse effects. Dose reduction was required in 8 of the 10 patients, but none discontinued therapy. The majority had stable disease (n=17). Gastric and small bowel oedema was evident in symptomatic patients after a median time of 67 weeks’ treatment. Histological correlation in five patients revealed mucosal oedema correlating with radiological evidence of congestion and oedema.</p> <p><strong>Discussion: </strong></p> <p>Gastrointestinal AEs with selpercatinib may be more common than previously described. Most are self-limiting but often require dose adjustments. Histological evidence of mucosal oedema observed in conjunction with the radiological findings of congestion and wall thickening suggest that bowel wall oedema is a predominant mechanism of abdominal pain in these patients.</p>
All-atom molecular dynamics simulations of phenylalanine-4-hydroxylase (PAH) tetramer to investigate the impact of two novel heterozygous mutations, p.Y198N and p.Y204F, observed in a classical phenylketonuria patient
<p>Phenylalanine-4-hydroxylase (PAH) tetramer system (Robetta modelling to complete the structure with template PDB ID: 6hyc) with parametrised BH<sub>4</sub> ligand (parameters are available in the dataset) and Fe(II) metal ions in a TIP3P water box ionised with 0.15 M KCl were presented as wild-type and carrying two novel mutations as Y198N on dimeric chains A and B, and Y204F on dimeric chains C and D. In addition, E353 and E422 are protonated as predicted by PROPKA. BH<sub>4</sub> molecule parametrization was performed by using GAFF, Antechamber and “amb2chm_par.py” program of Amber2018.</p> <p>5,000-step minimization and 1 ns equilibration were performed by fixing the protein to relax the system. Then, another 5,000-step minimization and 1 ns equilibration were performed without any constraints, except the SHAKE algorithm on water molecules, to relax the protein and system. The production simulations were performed along 100 ns trajectory at 310 K collected under NpT ensemble.</p> <p>All system preparation and simulation details for this dataset is available with the related background, results and conclusions in the following article:</p> <p>Tolga Aslan, Aslı Yenenler-Kutlu, Umut Gerlevik, Ayşe Çiğdem Aktuğlu Zeybek, Ertuğrul Kıykım, Osman Uğur Sezerman & Necla Birgul Iyison (2021) Identifying and elucidating the roles of Y198N and Y204F mutations in the PAH enzyme through molecular dynamic simulations, Journal of Biomolecular Structure and Dynamics, DOI: <a href="https://doi.org/10.1080/07391102.2021.1921619">10.1080/07391102.2021.1921619</a></p>
PSnpBind: A database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow
<p>A key concept in drug design is how natural variants, especially the ones occurring in the binding site of drug targets, affect the inter-individual drug response and efficacy by altering binding affinity. These effects have been studied on very limited and small datasets while, ideally, a large dataset of binding affinity changes due to binding site single-nucleotide polymorphisms (SNPs) is needed for evaluation. However, to the best of our knowledge, such a dataset does not exist. Thus, a reference dataset of ligands binding affinities to proteins with all their reported binding sites’ variants was constructed using a molecular docking approach. Having a large database of protein-ligand complexes covering a wide range of binding pocket mutations and a large small molecules’ landscape is of great importance for several types of studies. For example, developing machine learning algorithms to predict protein-ligand affinity or a SNP effect on it requires an extensive amount of data. In this work, we present PSnpBind: A large database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow. It provides a web interface to explore and visualize the protein-ligand complexes and a REST API to programmatically access the different aspects of the database contents. PSnpBind is freely available at <a href="https://psnpbind.org">https://psnpbind.org</a>.<strong> </strong>The source code of the tools used in constructing PSnpBind is available on <a href="https://github.com/ammar257ammar/PSnpBind-Build">GitHub</a>.</p>
Functional precision profiling reveals non-mutational rewiring of kinase signaling networks in colorectal cancer
<p>Multi-omics profiling of colorectal cancer (CRC) patients and associated patient-derived organoids. Tumor organoids were characterized in steady-state and perturbed using kinase inhibitors.</p>
Supplementary Simulation Data for "Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases Through a Ser/Ile Double Mutation"
<p>Additional simulation data for "Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases Through a Ser/Ile Double Mutation", which has been submitted as a preprint to ChemRxiv.</p>
Raw and processed cell lines (melanomaC818/melanomaMUM-2B/SK-MEL-28) data for detecting DMKN's mutations in melanoma cancer
<p>Raw and processed cell lines (melanomaC818/melanomaMUM-2B/SK-MEL-28) data for detecting DMKN's mutations in melanoma cancer. This research was concluded that DMKN is a trigger of epithelial-mesenchymal transition-driven melanoma.</p>
The Relationship between LRP5 (rs556442 and rs638051) Polymorphisms and Mutation with Bone Metabolism in Xinjiang women with Type 2 Diabetes after Menopause(Table 1 and Table 2 Statistical Values of Analysis Process)
<p>The Relationship between LRP5 (rs556442 and rs638051) Polymorphisms and Mutation with Bone Metabolism in Xinjiang women with Type 2 Diabetes after Menopause(Table 1 and Table 2 Statistical Values of Analysis Process)</p>
Figure 9. Adding-Reducing mutation.-Neuroevolution Mechanism for Hidden Markov Model
<p>Adding a small value from one weight and decrement that value to another weight. The chosen<br> weights should be involved in summation of 1.0. Figure 9 shows an example, we add 0.001 from<br> one weight and decrement the same value from another weight.</p>
Figure 5. Mutation process. This is happened by decreasing 0.2 from Med-Cold probability and adding 0.2 to Med- Hot.-Genetic Algorithms Principles Towards Hidden Markov Model
<p>Figure 5 illustrates an example of mutation process. In Figure 5, Med-Cold:0.9 and Med-Hot:0.1<br> before mutation and become Med-Cold:0.7 and Med-Hot:0.3 after mutation. This is done by<br> decreasing 0.2 from Med-Cold probability and adding 0.2 to Med-Hot probability.</p>
Figure 11. Group mutation-Neuroevolution Mechanism for Hidden Markov Model
<p>This happens by swapping two complete groups with summation of 1.0 with the same criteria.<br> Figure 10 shows a case of this.</p>
Data from: Mutations in yeast are deleterious on average regardless of the degree of adaptation to the testing environment
<p>The role of spontaneous mutations in evolution depends on the distribution of their effects on fitness. Despite a general consensus that new mutations are deleterious on average, a handful of mutation accumulation experiments in diverse organisms instead suggest that of beneficial and deleterious mutations can have comparable fitness impacts, i.e., the product of their respective rates and effects can be roughly equal. We currently lack a general framework for predicting when such a pattern will occur. One idea is that beneficial mutations will be more evident in genotypes that are not well adapted to the testing environment. We tested this prediction experimentally in the laboratory yeast <em>Saccharomyces cerevisiae</em> by allowing nine replicate populations to adapt to novel environments with complex sets of stressors. After >1000 asexual generations interspersed with 41 rounds of sexual reproduction, we assessed the mean effect of induced mutations on yeast growth in both the environment to which they had been adapting and the alternative novel environment. The mutations were deleterious on average, with the severity depending on the testing environment. However, we find no evidence that the adaptive match between genotype and environment is predictive of mutational fitness effects.</p>
Figure 2 in Detection of the Trp-2027-Cys Mutation in Fluazifop-P-butyl-resistant Itchgrass (RottboelliO cochinchinensis) using High-Resolution Melting Analysis (HRMA)
Figure 2. Agarose gel (1,8%) showing polymerase chain reaction products (89 bp) of the chloroplastic acetyl-coenzyme A carboxylase gene carboxyl-transferase domain targeted by HRMA primers RottF and RottR.
Figure 5 in Detection of the Trp-2027-Cys Mutation in Fluazifop-P-butyl-resistant Itchgrass (RottboelliO cochinchinensis) using High-Resolution Melting Analysis (HRMA)
Figure 5. High-resolution melting analysis (HRMA) for detection of the Trp-2027-Cys mutation in Rottboellia cochinchinensis carboxyl-transferase domain of the acetylcoenzyme A carboxylase gene conferring resistance to fluazifop-P-butyl. (B) Normalized plot and (C) difference plot using susceptible (wild type) as the reference genotype.
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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.