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.
429
datasets available to search
ShareScore release 0.9.0
Dataset results
429 results for “multiple genes”
Frequency of FCGR3A Gene Polymorphisms in Patients With Neuromyelitis Optica Spectrum Disorders, Anti-oligodendrocyte Myelin Protein Antibody Disease, and Multiple Sclerosis.
ClinicalTrials.gov study NCT06865274. IPD Sharing: NO. Countries: 1. Publications: 30.
Genes and Environment in Multiple Sclerosis
ClinicalTrials.gov study NCT01353547. IPD Sharing: NO. Countries: 1. Publications: 1.
Aminoacyl-tRNA synthetase gene alignments from multiple Sileneae species generated from full-length transcripts using Iso-Seq and raw microscopy image files
Open the record for dataset details and reuse information.
Data from: Multiple large inversions and breakpoint rewiring of gene expression in the evolution of the fire ant social supergene
Open the record for dataset details and reuse information.
Data from: Bayesian species delimitation combining multiple genes and traits in a unified framework
Open the record for dataset details and reuse information.
Data from: Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow
Open the record for dataset details and reuse information.
Extensive hybridization reveals multiple coloration genes underlying a complex plumage phenotype
Open the record for dataset details and reuse information.
Multiple paths to cold tolerance: the role of environmental cues, morphological traits and the circadian clock gene vrille
Open the record for dataset details and reuse information.
Additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum
Open the record for dataset details and reuse information.
Data from: Combinations of Spok genes create multiple meiotic drivers in Podospora
Open the record for dataset details and reuse information.
Alu-Mediated MEN1 Gene Deletion and Loss of Heterozygosity in a Patient with Multiple Endocrine Neoplasia Type 1
<p>Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disorder caused by mutations of the tumor suppressor gene <i>MEN1</i>. Most of the germline <i>MEN1</i> gene mutations have been small mutations, and the whole gene deletion is rarely observed. In the present study, we revealed <i>Alu </i>retrotransposon-mediated <i>de novo</i> germline deletion of the whole <i>MEN1</i> gene and somatic copy-neutral loss of heterozygosity (LOH) in a patient with MEN1. The patient is a 39-year-old woman who was referred to our department for the management of prolactinoma. She was also diagnosed with primary hyperparathyroidism and suspected of MEN1. Although nucleotide sequencing did not detect any <i>MEN1</i> gene mutations, multiplex ligation-dependent probe amplification (MLPA) revealed a large germline deletion of the <i>MEN1</i> gene. Subsequent quantitative polymerase chain reaction (qPCR)-based copy number mapping showed a monoallelic loss of approximately 18.5-kilobase region containing the whole <i>MEN1</i> gene. Intriguingly, the two breakpoints were flanked by <i>Alu</i> repetitive elements, suggesting the contribution of <i>Alu</i>/<i>Alu</i>-mediated rearrangements to the whole <i>MEN1 </i>gene deletion. Furthermore, copy number mapping using MLPA and qPCR in combination with single nucleotide polymorphism analysis revealed copy-neutral LOH as a somatic event for parathyroid tumorigenesis. In conclusion, copy number mapping revealed a novel combination of <i>Alu</i>/<i>Alu</i>-mediated <i>de novo</i> germline deletion of the <i>MEN1</i> gene and somatic copy-neutral LOH as a cytogenetic basis for the MEN1 pathogenesis. Moreover, subsequent <i>in silico</i> analysis highlighted the possible predisposition of the <i>MEN1 </i>gene to <i>Alu </i>retrotransposon-mediated genomic deletion.</p>
Figure 6 from: Wang L-H, Liu S, Tang Y-J, Chen Y-P, Wu J, Li J-L (2020) Using the combined gene approach and multiple analytical methods to improve the phylogeny and classification of Bombus (Hymenoptera, Apidae) in China. ZooKeys 1007: 1-21. https://doi.org/10.3897/zookeys.1007.34105
Figure 6 Phylogenetic relationships of the subgenera of Bombus from the Bayesian Inference tree (Fig. 2); nearly all of them are well supported by posterior probabilities.
Figure 4 from: Wang L-H, Liu S, Tang Y-J, Chen Y-P, Wu J, Li J-L (2020) Using the combined gene approach and multiple analytical methods to improve the phylogeny and classification of Bombus (Hymenoptera, Apidae) in China. ZooKeys 1007: 1-21. https://doi.org/10.3897/zookeys.1007.34105
Figure 4 Estimated phylogeny of the same samples using both new sequences and sequences from Cameron et al. (2007), based on five combined gene sequences (mitochondrial gene 16S rRNA, nuclear genes Opsin, ArgK, EF-1α, and PEPCK) analyzed by Maximum Likelihood. Values on the branches are the bootstrap values, (C) represents Cameron et al.'s species, and "BG" represents our species. The bold font indicates species from both datasets that did not cluster together into monophyletic clades.
Supplementary material 1 from: Wang L-H, Liu S, Tang Y-J, Chen Y-P, Wu J, Li J-L (2020) Using the combined gene approach and multiple analytical methods to improve the phylogeny and classification of Bombus (Hymenoptera, Apidae) in China. ZooKeys 1007: 1-21. https://doi.org/10.3897/zookeys.1007.34105
Key to the 26 species of the genus Bombus
Figure 2 from: Wang L-H, Liu S, Tang Y-J, Chen Y-P, Wu J, Li J-L (2020) Using the combined gene approach and multiple analytical methods to improve the phylogeny and classification of Bombus (Hymenoptera, Apidae) in China. ZooKeys 1007: 1-21. https://doi.org/10.3897/zookeys.1007.34105
Figure 2 Estimated phylogeny of Bombus based on six combined gene sequences (mitochondrial genes 16S rRNA and COI, nuclear genes Opsin, ArgK, EF-1α, and PEPCK) analyzed by Bayesian Inference and Maximum Likelihood. Subgeneric clades are noted at the right of the figure, values above branches are posterior probabilities (BI), values below branches are bootstrap values (ML). Species in bold font were collected by the authors in China and a black spot indicates species that were not included in the previous phylogeny of Bombus of Cameron et al. (2007). The outgroups are at the top of the tree. Abbreviations: SF, short-faced clade; LF, long-faced clade. Subgenera that were synonymized are in parentheses.
Figure 3 from: Wang L-H, Liu S, Tang Y-J, Chen Y-P, Wu J, Li J-L (2020) Using the combined gene approach and multiple analytical methods to improve the phylogeny and classification of Bombus (Hymenoptera, Apidae) in China. ZooKeys 1007: 1-21. https://doi.org/10.3897/zookeys.1007.34105
Figure 3 Estimated phylogeny of Bombus based on six combined gene sequences (mitochondrial genes 16S rRNA and COI, nuclear genes Opsin, ArgK, EF-1α, and PEPCK) analyzed by Maximum Parsimony. Subgeneric clades are noted at the right of the figure and values on branches are the bootstrap values. Species in bold font were collected in China and a black spot indicates species that were not included in the phylogeny of Bombus of Cameron et al. (2007). The outgroups are at the top of the tree. Abbreviations: SF, short-faced clade; LF, long-faced clade. Subgenera that were synonymized are in parentheses.
Figure 5 from: Wang L-H, Liu S, Tang Y-J, Chen Y-P, Wu J, Li J-L (2020) Using the combined gene approach and multiple analytical methods to improve the phylogeny and classification of Bombus (Hymenoptera, Apidae) in China. ZooKeys 1007: 1-21. https://doi.org/10.3897/zookeys.1007.34105
Figure 5 Estimated phylogeny of Bombus based on six combined gene sequences (mitochondrial genes 16S rRNA and COI, nuclear genes Opsin, ArgK, EF-1α, and PEPCK) analyzed by Neighbor Joining. Subgeneric clades are noted at the right of the Figure, and values on branches are the bootstrap values of NJ. Species in bold font were collected in China and a black spot indicates species that were not included in the phylogeny of Bombus of Cameron et al. (2007). The outgroups are at the bottom of the tree. Subgenera that were synonymized are in parentheses.
Data from: Molecular phylogenetics of Braconidae (Hymenoptera: Ichneumonoidea) based on multiple nuclear genes and implications for classification
This study examined subfamilial relationships within Braconidae, using 4kb of sequence data for 139 taxa. Genetic sampling included previously used markers for phylogenetic studies of Braconidae (28S and 18S rDNA) as well as new nuclear protein-coding genes (CAD and ACC). Maximum likelihood and Bayesian inference of the concatenated dataset recovered a robust phylogeny, particularly for early divergences within the family. This study focused primarily on non-cyclostome subfamilies, but the monophyly of the cyclostome complex was strongly supported. There was evidence supporting an independent clade, termed the aphidioid complex as sister to the cyclostome complex of subfamilies. Maxfischeria was removed from Helconinae and placed within its own subfamily within the aphidioid complex. Most relationships within the cyclostome complex were poorly supported, likely due to lower taxonomic sampling within this group. Similar to other studies, there was strong support for the alysioid subcomplex containing Gnamptodontinae, Alysiinae, Opiinae, and Exothecinae. Cenocoeliinae was recovered as sister to all other subfamilies within the euphoroid complex. Planitorus and Mannokeraia, previously placed in Betylobraconinae and Masoninae, respectively, were moved to the Euphorinae and may share a close affiliation with Neoneurinae. Neoneurinae and Ecnomiinae were placed as tribes within Euphorinae. A sister relationship between the microgastroid and sigalphoid complexes was also recovered. Within the helconoid complex was a well-supported lineage parasitic on lepidopteran larvae (macrocentroid subcomplex). Helconini was raised to subfamily status and was recovered as sister to the macrocentroid subcomplex. Blacinae was demoted to tribal status and placed within the newly circumscribed subfamily Brachistinae, which also contains the tribes Diospilini, Brulleiini, and Brachistini, all formerly in Helconinae.
Data from: Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference
Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong interest in identifying and removing unreliable parts of the alignment. In recent years several automated filtering approaches have been proposed, but despite their popularity, a systematic and comprehensive comparison of different alignment filtering methods on real data has been lacking. Here, we extend and apply recently introduced phylogenetic tests of alignment accuracy on a large number of gene families and contrast the performance of unfiltered versus filtered alignments in the context of single-gene phylogeny reconstruction. Based on multiple genome-wide empirical and simulated data sets, we show that the trees obtained from filtered MSAs are on average worse than those obtained from unfiltered MSAs. Furthermore, alignment filtering often leads to an increase in the proportion of well-supported branches that are actually wrong. We confirm that our findings hold for a wide range of parameters and methods. Although our results suggest that light filtering (up to 20% of alignment positions) has little impact on tree accuracy and may save some computation time, contrary to widespread practice, we do not generally recommend the use of current alignment filtering methods for phylogenetic inference. By providing a way to rigorously and systematically measure the impact of filtering on alignments, the methodology set forth here will guide the development of better filtering algorithms.
Data from: Exploring data interaction and nucleotide alignment in a multiple gene analysis of Ips (Coleoptera: Scolytinae)
The possibility of gene tree incongruence in a species-level phylogenetic analysis of the genus Ips (Coleoptera: Scolytidae) was investigated based on mitochondrial 16S rRNA and nuclear Elongation factor-1α sequences, and existing Cytochrome Oxidase I and non-molecular data sets. Separate cladistic analyses of the data partitions resulted in partially discordant most-parsimonious trees but revealed only low conflict of the phylogenetic signal. Interactions among data partitions, which differed in the level of sequence divergence (COI > 16S > EF-1α), base composition, and homoplasy, revealed that much of the branch support only emerges in the simultaneous analysis, in particular for deeper nodes in the tree which are almost entirely supported due to "hidden support" (sensu Gatesy et al., 1999). Apparent incongruence between data partitions is in part due to suboptimal alignments and bias of character transformations, but there is little evidence to invoke incongruent phylogenetic histories of genetic loci. There is also no justification for eliminating or downweighting gene partitions based on their level of homoplasy or apparent incongruence with other partitions, as the signal only emerges in the interaction of all data. In comparison to the traditional taxonomy, the pini, plastographus and perturbatus groups are polyphyletic, whereas the grandicollis group is monophyletic except for the inclusion of the (monophyletic) calligraphus group. The latidens group and some European species are distantly related and closer to other genera within Ipini. Our robust cladogram was used to revise the classification of Ips. We provide new diagnoses for Ips and four subgeneric taxa.
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.