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9 results for “trans eQTL”
Trans-eQTL effects on risk of type 1 diabetes: a test of the sparse effector (omnigenic) hypothesis of complex trait genetics (supplementary data)
<p>This repository contains summary-level data generated by performing <a href="https://github.com/molepi-precmed/trans-qtls">Genomewide aggregated trans- effects (GATE) analysis</a> in case-control study of Type 1 Diabetes (T1D).</p>
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: Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes
Previous studies had shown that integration of genome wide expression profiles, in metabolic tissues, with genetic and phenotypic variance, provided valuable insight into the underlying molecular mechanisms. We used RNA-Seq to characterize hypothalamic transcriptome in 99 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP), a reference resource population for cardiovascular and metabolic traits. We report numerous novel transcripts supported by proteomic analyses, as well as novel non coding RNAs. High resolution genetic mapping of transcript levels in HMDP, reveals both local and trans expression Quantitative Trait Loci (eQTLs) demonstrating 2 trans eQTL 'hotspots' associated with expression of hundreds of genes. We also report thousands of alternative splicing events regulated by genetic variants. Finally, comparison with about 150 metabolic and cardiovascular traits revealed many highly significant associations. Our data provides a rich resource for understanding the many physiologic functions mediated by the hypothalamus and their genetic regulation.
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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Data from: Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes
Open the record for dataset details and reuse information.
Dissecting the Genetics of the Human Transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci
GEO Series GSE65907. Homo sapiens. 2112 samples. Type: Expression profiling by array.
Lead Modulates trans- and cis-eQTLs in Drosophila melanogaster Heads
GEO Series GSE83141. Drosophila melanogaster. 158 samples. Type: Expression profiling by high throughput sequencing.
Co-expression trans-eQTL analysis data
<p><strong>Sample metadata:</strong></p> <ul> <li>sample_metadata.tsv - tab separated file with metadata for samples used in this analysis.</li> </ul> <p><strong>Gene expression matrix:</strong></p> <ul> <li>Merged_ENSG_expression.tsv - integrated gene expression matrix used in the co-expression analysis (Ensembl IDs in rows and sample IDs in columns). The matrix can be split into sub matrices using the metadata from sample_metadata.tsv for separate analysis of cell types.</li> </ul> <p><strong>Genes in the modules:</strong></p> <ul> <li>ICA_modules.tsv - data for assigning genes to modules from ICA method. Column 'loading' shows the contribution value of the gene to the module. Column 'approach' indicates if the module was detected from integrated or separate data. Column 'qtl_group' is an identifier for the cell type/condition.</li> <li>PEER_modules.tsv - data for assigning genes to modules from PEER method. Column 'loading' shows the contribution value of the gene to the module. </li> <li>PLIER_modules.tsv - data for assigning genes to modules from PLIER method. Column 'loading' shows the contribution value of the gene to the module.</li> <li>WGCNA_modules.tsv - data for assigning genes to modules from WGCNA method. Column 'loading' shows the contribution value of the gene to the module. Column 'loading' has value 1 as the method assigns genes to modules without defining their contributions. </li> <li>funcExplorer_modules.tsv - data for assigning genes to modules from funcExplorer method. Column 'loading' has value 1 as the method assigns genes to modules without defining their contributions. </li> </ul> <p><strong>Module eigenvectors used for the trans-eQTL analysis</strong></p> <ul> <li>eigenvectors_integrated.tsv - module eigenvectors for all the co-expression analysis methods applied to integrated data</li> <li>eigenvectors_separate.tsv- module eigenvectors for all the co-expression analysis methods applied to cell types separately</li> </ul> <p><strong>SuSiE fine mapping credible sets </strong></p> <ul> <li>SuSiE_credible_sets_integrated.tsv</li> <li>SuSiE_credible_sets_separate.tsv</li> </ul>
RNA-Sequencing of LPS-stimulated TLR4 HEK293 cells edited at an immune-response trans-eQTL locus
GEO Series GSE145486. Homo sapiens. 78 samples. Type: Expression profiling by high throughput sequencing.
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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.
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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.