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65 results for “regulatory links”
Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance
<p>The below data are associated with our paper entitled "Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance."</p> <p>1) SNP-gene link predictions generated by pgBoost and existing methods SCENT (Sakaue et al. 2024 <em>Nat Genet</em>), Signac (Stuart et al. 2021 <em>Nat Methods</em>), ArchR (Granja et al. 2021 <em>Nat Genet</em>), and Cicero (Pliner et al. 2018 <em>Mol Cell</em>).</p> <p><strong>pgBoost_scores.tsv.gz </strong>contains linking predictions made by pgBoost.</p> <p><strong>constituent_method_scores.tsv.gz</strong> contains linking predictions made by constituent methods.</p> <p><em><span>**NOTE: promoters (+/- 1kb from TSS) and candidate links >500kb are excluded from linking predictions (see manuscript)**</span></em></p> <p>Linking scores and percentiles are reported for each method (pgBoost score, SCENT FDR, Signac correlation, ArchR correlation, Cicero co-accessibility). Rank percentiles are computed as: 1 - (rank / n). When multiple links receive the same score, they are assigned the percentile of the top rank. Links unscored by each method (denoted by zeros* in the linking score column) are assigned a percentile equivalent to the percent of links unscored by the focal method. See the Methods section of the paper for further details on computing linking scores and summarizing scores across cell types and data sets.</p> <p>*Candidate links tested and assigned a co-accessibility of zero by the Cicero method are given a score of 1e-100 in the "Cicero" column to distinguish between unscored candidate links and candidate links assigned a partial correlation of zero (see Pliner et al. 2018 <em>Mol Cell</em>).</p> <p><em>NOTE: The predictions associated with this release (version 2) were generated using an expanded set of data sets, an expanded training set, and corrected TSS coordinates.</em></p> <p>2) GWAS-derived evaluation SNP-gene link evaluation set.</p> <p><strong>gwas_evaluation.tsv</strong>: GWAS-derived evaluation SNP-gene link evaluation set. Column 1 provides SNP coordinates in the format <chr-start-end>. This evaluation framework was proposed by Weeks et al. 2024 <em>Nature Genetics</em> based on fine-mapping results from Kanai et al. <em>medrxiv</em> (see Methods: <em>Evaluation data sets</em> of Dorans et al.). "True" links (gold = 1) are non-coding variants fine-mapped to a focal trait (PIP > 0.1) with a coding variant for exactly one candidate gene within 1 Mb attaining PIP > 0.5 for the same trait. "False" links (gold = 0) are candidate SNP-gene pairs involving a SNP with a "true" link. This file of SNP-gene links was adapted from credible set-gene links <a href="https://github.com/Deylab999/GWAS_benchmark_IGVF/blob/bb91d08cc02d59cdd829eb1430569057ac26c5fe/V2G/ENCODE_E2G_2023/UKBiobank.ABCGene.anyabc.tsv">here</a> (the "truth" column defines true/false links) by identifying SNPs with PIP > 0.1 within each credible set-gene link.</p>
LERC: Linked Extended Regulatory Circuits dataset on interactions between transcription factors and genes
<p>Turtles files of the project: <a href="https://regulatorycircuits-lod.genouest.org/">https://regulatorycircuits-lod.genouest.org/</a><br> 808 samples-specific files<br> 394 tissues-specific files<br> 2 mapping (FMA and Uberon)<br> 1 graph of experimental context<br> 1 graph of metadata</p> <p> </p>
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes
<p>ATAC-seq peaks are in narrowPeak format. RNA-seq results are organized according to cell type. The normalized RPKM is reported for each gene in GENCODE 19. All data was mapped to hg19.</p>
Transcription factor occupancy is linked to DNA methylation turnover at active regulatory regions [Bisulfite-Seq]
GEO Series GSE39736. Mus musculus. 3 samples. Type: Methylation profiling by high throughput sequencing.
The phosphatase PTEN links platelets with immune regulatory functions of mouse T follicular helper cells
GEO Series GSE143698. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease.
GEO Series GSE253165. Mus musculus; Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease [NIH-3T3_K562_RNA_with_blocking]
GEO Series GSE253163. Homo sapiens; Mus musculus. 1 samples. Type: Expression profiling by high throughput sequencing.
Compendium of Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis
GEO Series GSE255326. Homo sapiens. 422 samples. Type: Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Compendium of Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis [mpra_wt]
GEO Series GSE302353. Homo sapiens. 10 samples. Type: Other.
ATAC-seq datasets for chromatin accessibility quantification in "Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems"
GEO Series GSE150589. Rattus norvegicus. 18 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes
GEO Series GSE113483. Homo sapiens. 39 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease [NIH-3T3_K562_RNA_without_blocking]
GEO Series GSE253161. Homo sapiens; Mus musculus. 1 samples. Type: Expression profiling by high throughput sequencing.
FOG2 modulates a TBX5/GATA4-co-ocupied atrial gene regulatory network linking heart failure to atrial fibrillation risk [ncRNA-Seq]
GEO Series GSE198786. Mus musculus. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Linking Transcriptomic Organization to the Regulatory Landscape of Cyanobacteria through Context-Based Network Analysis
GEO Series GSE72880. Picosynechococcus sp. PCC 7002. 8 samples. Type: Expression profiling by high throughput sequencing.
Compendium of Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis [RNA-seq]
GEO Series GSE255325. Homo sapiens. 52 samples. Type: Expression profiling by high throughput sequencing.
Compendium of Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis [crispr_flow]
GEO Series GSE302443. Homo sapiens. 21 samples. Type: Other.
RNA-seq datasets for enhancer RNA quantification in "Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems"
GEO Series GSE150499. Rattus norvegicus. 19 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human colorectal cancer risk [RNA-seq]
GEO Series GSE222769. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
FOG2 modulates a TBX5/GATA4-co-ocupied atrial gene regulatory network linking heart failure to atrial fibrillation risk [RNA-Seq]
GEO Series GSE198734. Mus musculus. 7 samples. Type: Expression profiling by high throughput sequencing.
Link between GRHL2 Motifs and Intratumor Heterogeneity of Cis-Regulatory Elements Results in Poor Outcome in Luminal Breast Cancer: A Single-cell Chromatin Accessibility Analysis
GEO Series GSE198639. Homo sapiens. 16 samples. Type: Genome binding/occupancy 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.