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.
318
datasets available to search
ShareScore release 0.9.0
Dataset results
318 results for “mutational analysis”
Dataset for Efficient, robust, and versatile fluctuation data analysis using MLE MUtation Rate calculator (mlemur)
<p>This file contains the R and C++ code used for simulating experiments, simulated fluctuation data, and the results of estimations used in the paper "Efficient, robust, and versatile fluctuation data analysis using MLE MUtation Rate calculator (mlemur)".</p>
gnomAD polymorphism and de novo mutation data for analysis of mutation rates in highly mutable gene classes
<p>We analyze the human mutation rate in three gene classes (IGK, RNU, and tRNA) which deviate from the expectations of a mutation rate model. We examine the distribution of allele frequencies for SNVs within these genes and we analyze the counts of de novo mutations stratified by whether the SNV was observed or not. </p> <p>{CHR}_IGK_SFS_v2_denovo.gz: allele frequencies, mutation rate estimates, and whether the de novo mutation was observed for IGK, RNU, and tRNA genes. Based on gnomAD v3. </p> <p>{CHR}_indiv_mu.csv: quality information for variants in these gene classes from the 1kg subset of gnomAD.</p> <p>"CHR", "POS", "REF", "ALT", "FILTER", "AC", "AN", "MQRankSum", "pab_max", "VQSLOD", "AB", "PN", "MR", "AR", "MG", "MC", "QUAL"</p> <p>all_variants_chr21_mu_h.csv.gz: all variants from chromosome 21 to use for comparing allele frequencies to those in our gene classes.</p> <p>21_indiv_mu_all.csv.gz: quality information from all variants on chromosome 21 from the 1kg subset of gnomAD to use for comparison with gene classes.</p> <p>"CHR", "POS", "REF", "ALT", "FILTER", "AC", "AN", "MQRankSum", "pab_max", "VQSLOD", "AB", "PN", "MR", "AR", "MG", "MC", "QUAL"</p> <p> </p>
Data and analysis scripts associated with the paper 'Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history''
<p><em>Eva Bons, Christine Leemann, Karin J. Metzner, Roland R. Regoes</em></p> <p>This repository contains all the data and analysis scripts associated with the paper 'Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history'</p> <p>See the readme after unpacking the .zip for a description of the files</p>
Putative mutations associated with tetracycline resistance detected in Treponema spp.- an analysis of 4,355 Spirochaetales genomes
<p>Supplementary Table 1–4, , as well as multiple sequence alignment files for 16S rRNA, rpsC, and rpsJ loci, have been deposited.</p> <p>Additionally, the archive contains a <code>scripts.txt</code> file that includes all custom Bash scripts used for:</p> <ul> <li> <p>rRNA gene detection and quantification using <em>Barrnap</em></p> </li> <li> <p>Genome quality assessment using <em>CheckM</em></p> </li> <li> <p>Gene-by-gene schema creation, allele calling, and cgMLST extraction using <em>chewBBACA</em></p> </li> <li> <p>GFF merging and wide-format transformation for summarizing rRNA copy number per genome</p> </li> </ul> <p>These materials are provided to ensure reproducibility of the analyses and to support further investigations into antimicrobial resistance in <em>Spirochaetales</em>.</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 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.
Figure 4 in Detection of the Trp-2027-Cys Mutation in Fluazifop-P-butyl-resistant Itchgrass (RottboelliO cochinchinensis) using High-Resolution Melting Analysis (HRMA)
Figure 4. High-resolution melting analysis (HRMA) for detection of mutation Trp-2027-Cys in Rottboellia cochinchinensis carboxyl-transferase domain of the acetyl-coenzyme A carboxylase gene conferring resistance to fluazifop-P-butyl. Three genotypes are included: wild type (homozygous TGG, susceptible), mutant homozygous (TGC, resistant), and artificial mutant heterozygous (TGG/TGC, possibly resistant). (A) Representative profiles of the melting curves (derivative melt curves), (B) normalized plot, and (C) difference plot using susceptible (wild type) as the reference genotype.
Figure 1 in Detection of the Trp-2027-Cys Mutation in Fluazifop-P-butyl-resistant Itchgrass (RottboelliO cochinchinensis) using High-Resolution Melting Analysis (HRMA)
Figure 1. Sequence alignment showing the single-nucleotide change (G/C) within the chloroplastic acetyl-coenzyme A carboxylase gene carboxyl-transferase domain fragments from Rottboellia cochinchinensis susceptible (G) and resistant (C) biotypes. The sequences of the HRMA primers are colored in red. Position numbers (Alopecurus myosuroides full ACCase sequence, GenBank AJ310767, numbering) are given above the nucleotide sequences. Conserved nucleotides are indicated by dots.
Comprehensive Single Point Mutational Landscape Analysis of the Monkeypox Virus Proteome
Open the record for dataset details and reuse information.
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>
Binding of Cholesterol to the N-terminal Domain of the NPC1L1 Transporter: Analysis of the Epimerisation-Related Binding Selectivity and Loop Mutations
<p>Input files, topologies and trajectories of the work "Binding of Cholesterol to the N-terminal Domain of the NPC1L1 Transporter: Analysis of the Epimerisation-Related Binding Selectivity and Loop Mutations". </p>
Transcriptomic Analysis Data for MSTN Mutations and Mechanisms of Muscle Hypertrophy in a New Guinea Pig Breed
<p>This dataset contains raw RNA-seq data from six guinea pig muscle samples, split into two groups:</p> <ul> <li><strong>Native guinea pigs (B1 to B3):</strong> Control group with no selective breeding.</li> <li><strong>Kuri breed guinea pigs (B4 to B6):</strong> Synthetic hybrid group selectively bred for increased muscle mass.<br>Each sample has paired-end FASTQ files (e.g., B1_1.fq.gz and B1_2.fq.gz).</li> </ul>
Mutational Profiling in Epithelial Ovarian Cancer: A Meta-Analysis of 435 Patients Dataset
<p><strong>Data Description</strong></p> <p>0 represents no mutation, 1 represents a mutation</p> <p>Survive relates to the survival outcome of the patient. SurviveTime is in days (7300 chosen for alive patients).</p> <p>Ovarian Cancer Patients</p> <ul> <li>361 count</li> <li>TP53, BRCA1, BRCA2, KMT2C, CDK12, CSMD3, TTN, MUC16, NF1, PALB2, RB1, PTEN, FOXM1, BRIP1, KRAS, RASA1, CHEK2, RAD50, RAD51C/D, MRE11A, NBN, FANCE, FANCD2, ATR, ATM, MSH2, PMS2, MLH1, MSH6, FAT1, FAT2, FAT3, FAT4</li> </ul> <p>Uterine Cancer Patients</p> <ul> <li>437 count</li> <li>MSH6, CDK12, PMS2, BRIP1, FAT1, CSMD3, FAT4, BRCA2, MUC16, PALB2, KRAS, BRCA1, MSH2, PTEN, TP53, NF1, KMT2C, FAT3, FANCD2, ATM, NBN, ATR, CHEK2, FANCE, MLH1</li> </ul> <p>Cervical Cancer Patients</p> <ul> <li>174 count</li> <li>CSMD3, CDK12, FAT1, BRIP1, RB1, FAT4, BRCA2, MUC16, PALB2, KRAS, TP53, PTEN, KMT2C, FAT3, BRCA1, NF1, ATM, FANCD2, NBN, ATR, MLH1</li> </ul>
Supplementary Materials for: A Comprehensive Cohort Analysis Comparing Growth and GH Therapy Response in IGF1R Mutation Carriers and SGA Children
<p>Supplemental Tables and Figures for the clinical research article: <strong>A Comprehensive Cohort Analysis Comparing Growth and GH Therapy Response in IGF1R Mutation Carriers and SGA Children</strong></p>
Data accompanying "In silico analysis of the profilaggrin sequence indicates alterations in the stability, degradation route, and intracellular protein fate in filaggrin null mutation carriers" article.
<p>This research was supported by the National Science Centre, Poland, grant PRELUDIUM number 2021/41/N/NZ1/03473 to NS, National Science Centre, Poland, grant SONATA BIS number 2019/34/E/NZ6/00354 to DG-O, as well as POIR.04.04.00-00-21FA/16–00 grant, carried out within the First TEAM programme of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund (awarded to DG-O). WP was supported by the National Science Centre, Poland, grant SONATA-BIS number 2021/42/E/NZ1/00190. SB is supported by a Wellcome Trust Senior Research Fellowship (220875/Z/20/Z).</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>
Analysis of rod-cone dystrophy genes reveals unique mutational patterns
<div> Background <p>Rod-cone dystrophy (RCD) is the most common inherited retinal disease that is characterised by the progressive degeneration of retinal photoreceptors. RCD genes' classification is based exclusively on gene mutations' prevalence and does not consider the implication of the same gene in different phenotypes. Therefore, we first investigated the mutations occurrence in autosomal recessive RCD (arRCD) and non-arRCD conditions. Then, finally, we identified arRCD enriched mutational patterns in specific genes and coding exons<strong>.</strong></p> </div> Methods and results <p>The mutations' patterns differed according to arRCD (p=0.001). Specifically, When compared with missense; insertions/deletions (OR=1.2, p=0.007), nonsense (OR=1.2, p=0.014) and splice-site mutations (OR=1.6, p=0.038) increased the OR of arRCD by 20%–60% versus non-arRCD conditions. The gene-based analysis identified that EYS, IMPG2, RP1L1 and USH2A mutations were enriched in arRCD (p<0.05). The exon-based analysis revealed specific mutation patterns in exons of CRB1, RP1L1 and exons 12, 60 and 62 coding for Lamin EGF and FTIII domains of USH2A.</p> <p></p> <div> Conclusion <p>The current analysis showed that many aRCD genes have unique mutational patterns.</p> </div>
Comparative analysis of two Candida parapsilosis isolates from the patient with a central venous catheter harbouring the Y132F and R398I mutations
<p>This work presents a comparative analysis of 2 clinical isolates of <em>C. parapsilosis</em>; isolated from haemoculture (HC) and central venous catheter (CVC). Both strains harboured Y132F and R398I mutations associated with resistance to fluconazole (FLC). Differences between HC and CVC isolates in terms of virulence, resistance to FLC and lipid distribution were addressed. Expression of the ERG6 and ERG9 genes, lipid analysis, fatty acid composition and lipase activity were assessed by qPCR, thin-layer chromatography/high performance liquid chromatography, gas chromatography and spectrophotometry, respectively. A regulation of the ERG6 and ERG9 genes did not prove any impact on FLC resistance. Analysis of lipid metabolism showed a higher accumulation of lanosterol in both isolates regardless of FLC presence. Additionally, a decreased level in triacylglycerols (TAG) with impact on the composition of total FA was observed for both isolates. Direct impact of the ERG11 mutations to lipid/FA analysis has not been confirmed. The higher lipase activity observed for <em>C. parapsilosis</em> HC isolate could be correlated with the significantly decreased level of TAG. The very close relatedness between both isolates suggests that one isolate was derived from another after the initial infection of the host.</p>
Evaluation Data - Systematic Assessment of Fuzzers using Mutation Analysis
<p>The Databases which contain the results of the experiments done for the paper: "Systematic Assessment of Fuzzers using Mutation Analysis"</p> <p>Contained are the databases for the basic, ASan, and 24 hour runs under the data directory. The seed<em> </em>corpora are found in the directory seeds, minimal directory contains the initial seeds used for coverage fuzzing, the coverage directory contains the seeds that resulted from coverage fuzzing.</p> <p>To reproduce the results in the paper from scratch all that is required is the seed/minimal directory, all other artifacts are produced from this data.</p> <p>Additionally, the results of the two manual analyses are contained: not_killed_24.xlsx contain the notes of the manual analysis of unkilled mutants even after the 24 hour experiment, see Section 5.2.1. CVEs.xlsx are the notes taken during for the manual analysis of which CVEs can be reproduced mutants as described in Section 5.4. The script to collect the CVEs is provided as well under cve-script.7z.</p>
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.