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50 results for “overlapping genes”
Overlap of vitamin A and vitamin D target genes with CAKUT-related processes
<p>Underlying data of our study "<a href="http://doi.org/10.12688/f1000research.51018.2">Overlap of vitamin A and vitamin D target genes with CAKUT-related processes</a>" are provided here.</p> <p> </p> <p>Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) are a group of abnormalities affecting the kidneys and their outflow tracts. Vitamins are among the environmental factors that are considered for CAKUT aetiology. In this study, we collected vitamin A and vitamin D target genes and computed their overlap with CAKUT-related gene sets. We observed in particular significant overlaps between vitamin A target genes and CAKUT causal genes or genes involved in renal system development.</p>
Engineering gene overlaps to sustain genetic constructs in vivo
<p>Experimental data, simulation data, and code for data analysis and figure production for the paper "Engineering gene overlaps to sustain genetic constructs in vivo" (Decrulle, Frenoy, et al, PloS Computational Biology)</p>
Data from: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis
The opportunistic pathogens Staphylococcus aureus and Staphylococcus epidermidis represent major causes of severe nosocomial infection, and are associated with high levels of mortality and morbidity worldwide. These species are both common commensals on the human skin and in the nasal pharynx, but are genetically distinct, differing at 24% average nucleotide divergence in 1,478 core genes. To better understand the genome dynamics of these ecologically similar staphylococcal species, we carried out a comparative analysis of 324 S. aureus and S. epidermidis genomes, including 83 novel S. epidermidis sequences. A reference pan-genome approach and whole genome multilocus-sequence typing revealed that around half of the genome was shared between the species. Based on a BratNextGen analysis, homologous recombination was found to have impacted on 40% of the core genes in S. epidermidis, but on only 24% of the core genes in S. aureus. Homologous recombination between the species is rare, with a maximum of nine gene alleles shared between any two S. epidermidis and S. aureus isolates. In contrast, there was considerable interspecies admixture of mobile elements, in particular genes associated with the SaPIn1 pathogenicity island, metal detoxification, and the methicillin-resistance island SCCmec. Our data and analysis provide a context for considering the nature of recombinational boundaries between S. aureus and S. epidermidis and, the selective forces that influence realized recombination between these species.
FIGURE 2 in Mitochondrial genome of Poecilimon cretensis (Orthoptera: Tettigoniidae: Phaneropterinae): Strong phylogenetic signals in gene overlapping regions
FIGURE 2. Phylogenetic tree inferred by maximum likelihood using W-IQ-Tree from 13 Phaneropterinae mitogenomes representing different tribes (number along the nodes indicate bootstrap support).
Data from: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis
Open the record for dataset details and reuse information.
FIGURE 1 in Mitochondrial genome of Poecilimon cretensis (Orthoptera: Tettigoniidae: Phaneropterinae): Strong phylogenetic signals in gene overlapping regions
FIGURE 1. The map of mitochondrial genome and habitus of Poecilimon cretensis
The AHL- and BDSF-dependent quorum sensing systems control specific and overlapping sets of genes in Burkholderia cenocepacia H111
GEO Series GSE41244. Burkholderia cenocepacia H111. 3 samples. Type: Expression profiling by high throughput sequencing.
Modulation of gene expression by ZNF143, THAP11 and NOTCH1 via overlapping binding sites in mammalian cells
GEO Series GSE39263. Homo sapiens; Mus musculus. 17 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
PRD class homeobox genes in bovine early embryos: function, evolution and overlapping roles
GEO Series GSE192356. Bos taurus. 15 samples. Type: Expression profiling by high throughput sequencing.
Global transcriptional response of Methylorubrum extorquens to formaldehyde stress includes both overlapping and unique gene sets in comparison to antibiotic translational inhibition and expands the r
GEO Series GSE163955. Methylorubrum extorquens. 81 samples. Type: Expression profiling by high throughput sequencing.
Differential and overlapping effects of 20.23(OH)2D3 and 1,25(OH)2D3 on gene expression in human epidermal keratinocytes
GEO Series GSE117351. Homo sapiens. 9 samples. Type: Expression profiling by array.
Genes differentially expressed by Haemophilus ducreyi during anaerobic growth significantly overlap with those differentially expressed during experimental infection of human volunteers
GEO Series GSE193250. [Haemophilus] ducreyi. 24 samples. Type: Expression profiling by high throughput sequencing.
Time-dependent recruitment of GAF, ISGF3 and IRF1 complexes to GAS, ISRE and composite genes shapes IFNa and IFNg activated transcriptional responses and explains functional overlap [RNA-seq]
GEO Series GSE221804. Homo sapiens. 126 samples. Type: Expression profiling by high throughput sequencing.
Functional genomics identify distinct and overlapping genes mediating resistance to different classes of heterobifunctional degraders of oncoproteins
GEO Series GSE162205. Homo sapiens. 42 samples. Type: Expression profiling by high throughput sequencing.
Hand1 gene replacement with Hand2 reveals overlap in function with unique occurrence of omphalocele and heart defects [scRNA-seq]
GEO Series GSE299253. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
Time-dependent recruitment of GAF, ISGF3 and IRF1 complexes to GAS, ISRE and composite genes shapes IFNa and IFNg activated transcriptional responses and explains functional overlap [CHIP-seq]
GEO Series GSE222667. Homo sapiens. 82 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells [RNA-seq]
GEO Series GSE144115. Mus musculus. 15 samples. Type: Expression profiling by high throughput sequencing.
Overlapping gene regulation by cytosine methylation and histone deacetylation
GEO Series GSE1612. Arabidopsis thaliana. 13 samples. Type: Expression profiling by array.
miR-124, -128 and -137 orchestrate neural differentiation by acting on overlapping gene sets containing a highly connected transcription factor network
GEO Series GSE67135. Mus musculus. 27 samples. Type: Expression profiling by high throughput sequencing.
Parallel high-throughput RNA-sequencing suggests little overlap of differential gene expression between knockout of TDP-43 and its over-expression in central nervous system in Drosophila
GEO Series GSE31194. Drosophila melanogaster. 14 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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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.