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Dataset results
294 results for “Gene Sets”
Data from: Scanning SNPs from a large set of expressed genes to assess the impact of artificial selection on the undomesticated genetic diversity of white spruce
A scan involving 1134 single-nucleotide polymorphisms (SNPs) from 709 expressed genes was used to assess the potential impact of artificial selection for height growth on the genetic diversity of white spruce. Two case populations of different sizes simulating different family selection intensities (K = 13% and 5%, respectively) were delineated from the Quebec breeding program. Their genetic diversity and allele frequencies were compared with those of control populations of the same size and geographic origin to assess the effect of increasing the selection intensity. The two control populations were also compared to assess the effect of reducing the sampling size. On one hand, in all pairwise comparisons, genetic diversity parameters were comparable and no alleles were lost in the case populations compared with the control ones, except for few rare alleles in the large case population. Also, the distribution of allele frequencies did not change significantly (P ≤ 0.05) between the populations compared, but ten and nine SNPs (0.8%) exhibited significant differences in frequency (P ≤ 0.01) between case and control populations of large and small sizes, respectively. Results of association tests between breeding values for height at 15 years of age and these SNPs supported the hypothesis of a potential effect of selection on the genes harboring these SNPs. On the other hand, contrary to expectations, there was no evidence that selection induced an increase in linkage disequilibrium in genes potentially affected by selection. These results indicate that neither the reduction in the sampling size nor the increase in selection intensity was sufficient to induce a significant change in the genetic diversity of the selected populations. Apparently, no loci were under strong selection pressure, confirming that the genetic control of height growth in white spruce involves many genes with small effects. Hence, selection for height growth at the present intensities did not appear to compromise background genetic diversity but, as predicted by theory, effects were detected at a few gene SNPs harboring intermediate allele frequencies.
Data from: A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering
Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used multiple sequence alignments from over 600 angiosperms for 353 putatively single-copy protein-coding genes identified by the One Thousand Plant Transcriptomes Initiative to design a set of targeted sequencing probes for phylogenetic studies of any angiosperm group. To maximize the phylogenetic potential of the probes while minimizing the cost of production, we introduce a k-medoids clustering approach to identify the minimum number of sequences necessary to represent each coding sequence in the final probe set. Using this method, five to 15 representative sequences were selected per orthologous locus, representing the sequence diversity of angiosperms more efficiently than if probes were designed using available sequenced genomes alone. To test our approximately 80,000 probes, we hybridized libraries from 42 species spanning all higher-order groups of angiosperms, with a focus on taxa not present in the sequence alignments used to design the probes. Out of a possible 353 coding sequences, we recovered an average of 283 per species and at least 100 in all species. Differences among taxa in sequence recovery could not be explained by relatedness to the representative taxa selected for probe design, suggesting that there is no phylogenetic bias in the probe set. Our probe set, which targeted 260 kbp of coding sequence, achieved a median recovery of 137 kbp per taxon in coding regions, a maximum recovery of 250 kbp, and an additional median of 212 kbp per taxon in flanking non-coding regions across all species. These results suggest that the Angiosperms353 probe set described here is effective for any group of flowering plants and would be useful for phylogenetic studies from the species level to higher-order groups, including the entire angiosperm clade itself.
PP2A complex disruptor SET prompts widespread hyper-transcription of growth-essential genes in the pancreatic cancer cells
<p>Hyper-activation of the oncogenic transcription reflects the epigenetic plasticity of the cancer cells. SET was described as a nuclear factor that stimulated transcription from the chromatin template. However, the mechanisms of SET-dependent transcription are unknown. Here, we found that over-expression of SET and CDK9 induced very similar transcriptome signatures in multiple cancer cell lines. SET localized in the transcription start site (TSS)-proximal regions and supported the RNA transcription. SET specifically bound the PP2A-C subunit and induced PP2A-A subunit repulsion from the C subunit, which indicated the role of SET as a PP2A-A/C complex disruptor in the TSS-proximal regions. Through blocking PP2A activity, SET assisted CDK9 to maintain Pol II CTD phosphorylation and activated mRNA transcription. Our findings position SET as a key factor that modulates chromatin PP2A activity, promoting the oncogenic transcription in pancreatic cancer.</p>
A method for identifying environmental stimuli and genes responsible for genotype-by-environment interactions from a large-scale multi-environment data set
<p>It has not been fully understood in real fields what environment stimuli cause the genotype-by-environment (G × E) interactions, when they occur, and what genes react to them. Large-scale multi-environment data sets are attractive data sources for these purposes because they potentially experienced various environmental conditions. In this study, we developed a data-driven approach termed <u>E</u>nvironmental <u>C</u>ovariate Search Affecting <u>G</u>enetic <u>C</u>orrelations (ECGC) to identify environmental stimuli and genes responsible for the G × E interactions from large-scale multi-environment data sets. ECGC was applied to a soybean (<i>Glycine max</i>) data set that consisted of 25,158 records collected at 52 environments. ECGC illustrated what meteorological factors shaped the G × E interactions in six traits including yield, flowering time, and protein content and when they were involved. For example, it illustrated the relevance of precipitation around sowing dates and hours of sunshine just before maturity to the interactions observed for yield. Moreover, genome-wide association mapping on the sensitivities to the identified stimuli discovered candidate and known genes responsible for the G × E interactions. Our results demonstrate the capability of data-driven approaches to bring novel insights on the G × E interactions observed in fields. This dataset provides the data used in this study and supplementary tables cited in the manuscript.</p>
A new gene set identifies senescent cells and predicts senescence-associated pathways across tissues
<p>Although cellular senescence drives multiple age-related co-morbidities through the senescence-associated secretory phenotype (SASP), <em>in vivo</em> senescent cell identification remains challenging. Here, we generated a gene set (SenMayo) and validated its enrichment in bone biopsies from two aged human cohorts. We further demonstrated reductions in SenMayo in bone following genetic clearance of senescent cells in mice and in adipose tissue from humans following pharmacological senescent cell clearance. We next used SenMayo to identify senescent hematopoietic or mesenchymal cells at the single cell level from human and murine bone marrow/bone scRNA-seq data. Thus, SenMayo identifies senescent cells across tissues and species with high fidelity. Using this senescence panel, we were able to characterize senescent cells at the single-cell level and identify key intercellular signaling pathways. SenMayo also represents a potentially clinically applicable panel for monitoring senescent cell burden with aging and other conditions as well as in studies of senolytic drugs.</p>
Analysis of opposing histone modifications H3K4me3 and H3K27me3 reveals candidate diagnostic biomarkers for triple negative breast cancer and gene set prediction combinations
<p>Supplementary data of manuscript <strong>'Analysis of opposing histone modifications H3K4me3 and H3K27me3 reveals candidate diagnostic biomarkers for triple negative breast cancer and gene set prediction combinations </strong><strong>Analysis of opposing histone modifications H3K4me3 and H3K27me3 reveals candidate diagnostic biomarkers for triple negative breast cancer and gene set prediction combinations'</strong></p>
Liver transcriptome analysis reveals PSC-attributed gene set associated with fibrosis progression
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PP2A complex disruptor SET prompts widespread hyper-transcription of growth-essential genes in the pancreatic cancer cells
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A new gene set identifies senescent cells and predicts senescence-associated pathways across tissues
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Data from: Scanning SNPs from a large set of expressed genes to assess the impact of artificial selection on the undomesticated genetic diversity of white spruce
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A method for identifying environmental stimuli and genes responsible for genotype-by-environment interactions from a large-scale multi-environment data set
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Data from: A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering
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GSAn_Supplementary_Data: Description of the investigated gene sets
<p>The following table provides the number of genes in each BTM gene set [1] as well as the number of genes annotated within GOA and by each of the following tools: GSAn, DAVID [2], g:Profiler [3], ClusterProfiler [4] and WebGestalt [5].</p>
Table S2: Gene set enrichment analysis and KEGG
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Source code for ferroptosis gene set activity analysis in BLCA epithelial cells
<p>Source code for ferroptosis gene set activity analysis in BLCA epithelial cells </p>
Domain scanning results for a selected set of high-quality-annotation protein isoforms produced by human transcription factor genes
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DNA methylation of the natriuretic peptides system genes and ischemic stroke: gene-based and gene-set analyses
<p><span><b>Background</b></span></p> <p><span>The natriuretic peptides (NP) system has been considered an important regulator for ischemic stroke (IS) with a limited clinical implication. A better understanding of the underlying molecular mechanisms is urgent. Here, we aimed to examine the role of NP system genes methylation in IS.</span></p> <p><span><b>Methods and Results</b></span></p> <p><span>DNA methylation at promoter regions of four core NP system genes, e.g., <i>CORIN</i>, <i>FURIN</i>, <i>NPPA</i>, and <i>NPPB</i>, was measured by targeted bisulfite sequencing in 853 IS patients and 918 healthy controls. We first examined the association between DNA methylation at each single CpG and IS, followed by gene-based and gene-set analyses to examine the joint associations of DNA methylation at multiple CpGs in a gene or all four genes as a pathway with IS. After control of covariates and multiple testing, DNA methylation at 19 of the 36 assayed CpGs were individually associated with IS at q<0.05. The average methylation levels at the targeted regions of <i>CORIN</i> (OR=0.64, 95%CI: 0.56-0.73), <i>FURIN</i> (OR=0.78, 95%CI: 0.69-0.88), and <i>NPPA</i> (OR=0.78, 95%CI: 0.69-0.88) were inversely associated with IS (all q<0.05). The truncated product method revealed the same gene-based associations (all q<0.05) and found that DNA methylation at all four NP system genes together was jointly associated with IS (<i>P</i>=0.0001).</span></p> <p><span><b>Conclusions</b></span></p> <p><span>DNA methylation at NP system genes was downregulated in IS patients. Our results may unravel a molecular mechanism underlying the regulating effect of the NP system on IS, and highlight the relevance of testing the joint effect of multiple CpGs in the epigenetic analysis.</span></p>
The predicted haploid gene set of the genome of Nitzschia putrida
<p>Secondary loss of photosynthesis is observed across almost all plastid-bearing branches of the eukaryotic tree of life. However, genome-based insights into the transition from a phototroph into a secondary heterotroph have so far only been revealed for parasitic species. Free-living organisms can yield unique insights into the evolutionary consequence of the loss of photosynthesis, as the parasitic lifestyle requires specific adaptations to host environments. Here we report on the diploid genome of the free-living diatom <i>Nitzschia putrida </i>(35 Mbp), a non-photosynthetic osmotroph whose photosynthetic relatives contribute ca. 40% of net oceanic primary production. Comparative analyses with photosynthetic diatoms and heterotrophic algae with parasitic lifestyle revealed that a combination of gene loss, the accumulation of genes involved in organic carbon degradation, a unique secretome and the rapid divergence of conserved gene families involved in cell wall and extracellular metabolism appear to have facilitated the lifestyle of a free-living secondary heterotroph.</p>
Ensembl genes [data set for teaching purposes]
<p>CSV file for teaching purposes.</p>
Disease gene sets
<p>This file provides the risk genes for 14 diseases.</p>
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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.