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325 results for “Mediation analysis”
Data from: Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians
A large fraction of human genes are regulated by genetic variation near the transcribed sequence (cis-eQTL, expression quantitative trait locus), and many cis-eQTLs have implications for human disease. Less is known regarding the effects of genetic variation on expression of distant genes (trans-eQTLs) and their biological mechanisms. In this work, we use genome-wide data on SNPs and array-based expression measures from mononuclear cells obtained from a population-based cohort of 1,799 Bangladeshi individuals to characterize cis- and trans-eQTLs and determine if observed trans-eQTL associations are mediated by expression of transcripts in cis with the SNPs showing trans-association, using Sobel tests of mediation. We observed 434 independent trans-eQTL associations at a false-discovery rate of 0.05, and 189 of these trans-eQTLs were also cis-eQTLs (enrichment P<0.0001). Among these 189 trans-eQTL associations, 39 were significantly attenuated after adjusting for a cis-mediator based on Sobel P<10-5. We attempted to replicate 21 of these mediation signals in two European cohorts, and while only 7 trans-eQTL associations were present in one or both cohorts, 6 showed evidence of cis-mediation. Analyses of simulated data show that complete mediation will be observed as partial mediation in the presence of mediator measurement error or imperfect LD between measured and causal variants. Our data demonstrates that trans-associations can become significantly stronger or switch directions after adjusting for a potential mediator. Using simulated data, we demonstrate that this phenomenon is expected in the presence of strong cis-trans confounding and when the measured cis-transcript is correlated with the true (unmeasured) mediator. In conclusion, by applying mediation analysis to eQTL data, we show that a substantial fraction of observed trans-eQTL associations can be explained by cis-mediation. Future studies should focus on understanding the mechanisms underlying widespread cis-mediation and their relevance to disease biology, as well as using mediation analysis to improve eQTL discovery.
Data from: Living in a high CO2 world: a global meta-analysis shows multiple trait-mediated responses of fish to ocean acidification
Understanding how marine organisms will be affected by global change is of primary importance to ensure ecosystem functioning and nature contributions to people. This study meets the call for addressing how life-history traits mediate effects of ocean acidification on fish. We built a database of overall and trait-mediated responses of teleost fish to future CO2 levels by searching the scientific literature. Using a meta-analytical approach, we investigated the effects of projected CO2 levels by IPCC for 2050-2070 and 2100 on fish eco-physiology and behavior from 320 contrasts on 42 species, stemming from polar to tropical regions. Moreover, since organisms may experience a mosaic of carbonate chemistry in coastal environments (e.g. in estuaries, upwelling zones and intertidal habitats), which may have higher pCO2 values than open ocean waters, we assessed responses from additional 103 contrasts on 21 fish species using pCO2 levels well above IPCC projections. Under mid- and end-of-century CO2 emission scenarios, we found multiple CO2-dose dependent effects on calcification, resting metabolic rate, yolk, behavioral performances, along with increased predation risk and decreased foraging, particularly for larvae. Importantly, many of the traits considered will not confer fish tolerance to elevated CO2 and far-reaching ecological consequences on fish population replenishment and community structure will likely occur. Extreme CO2 levels well above IPCC projections showed effects on fish mortality and calcification, while growth, metabolism and yolk were unaffected. CO2 exposures in short-term experiments increased fish mortality, which in turn decreased in longer-term exposures. Whatever the elevated CO2 levels considered, some key biological processes (e.g. reproduction, development, habitat choice) resulted critically understudied. Fish are an important resource for livelihoods in coastal communities and a key component for stability of marine ecosystems. Given the multiple trait-mediated effects evidenced here, we stress the need to fill the knowledge gap on important eco-physiological processes and to expand the number and duration of ocean acidification studies to multi-generational, multiple stressor (e.g. warming, hypoxia, fishing) and species interactions experiments to better elucidate complex ecosystem-level changes and how these changes might alter provisioning of ecosystem services.
The mediating role of statistical anxiety in the relationship between statistical attitudes and statistical self-efficacy beliefs of students taking biostatistics courses: A path analysis
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Action Planning Makes Physical Activity More Automatic, Only If it Is Autonomously Regulated: A Moderated Mediation Analysis
<p>Dataset used for analysis. </p>
LC-MS analysis raw data of DTX3L-mediated enzymatic conjugation of ubiquitin with various nucleotide substrates
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Supplementary material 2 from: Cole MW (2018) Effectiveness of peer-mediated learning for English language learners: A meta-analysis. Research Ideas and Outcomes 4: e29375. https://doi.org/10.3897/rio.4.e29375
These are studies that were potentially-relevant to the meta-anlayses, but that were ultimately excluded during inclusion coding. Future researchers might find this list especially valuable.
Analysis of Biopsies With Antibody Mediated Rejection According to the Therapy Response
ClinicalTrials.gov study NCT03430414. IPD Sharing: Not stated. Countries: 0. Publications: 1.
Which enemies mediate distance- and density-dependent mortality of tree seeds and seedlings? A meta-analysis of fungicide, insecticide, and exclosure studies
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Data from: Living in a high CO2 world: a global meta-analysis shows multiple trait-mediated responses of fish to ocean acidification
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Data from: Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions
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Data from: Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians
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Transcriptome Analysis Reveals Extensive Alternative Splicing-Coupled Nonsense-Mediated mRNA Decay in a Human Cell Line
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Polysome fractionation analysis reveals features important for human nonsense-mediated mRNA decay
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Single-cell analysis reveals Mycobacterium tuberculosis ESX-1–mediated accumulation of permissive macrophages in infected mouse lungs
GEO Series GSE263880. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions
GEO Series GSE145530. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Global analysis of Upf1 in mESCs reveals expanded scope of nonsense-mediated mRNA decay
GEO Series GSE41785. Mus musculus. 23 samples. Type: Expression profiling by high throughput sequencing; Other.
Transcriptome analysis of vascular smooth muscle cells from mice deficient for chaperone-mediated autophagy
GEO Series GSE143162. Mus musculus. 4 samples. Type: Expression profiling by array.
Comparative transcriptome analysis between resistant and susceptible tomato lines uncovers the response mechanism of Cf-16-mediated resistance to Cladosporium fulvum
GEO Series GSE133678. Solanum lycopersicum. 24 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic analysis of the zebrafish inner ear points to growth hormone mediated regeneration following acoustic trauma
GEO Series GSE29669. Danio rerio. 9 samples. Type: Expression profiling by array.
Transcriptomic analysis of THAP1 mediated oligodendrocyte development
GEO Series GSE161556. Mus musculus. 18 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.