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120 results for “Functional analysis of genome”
Functional genomics analysis to disentangle the role of genetic variants in major depression - Supplementary Tables
<p>This entry contains the data generated by the study "Functional genomics analysis to disentangle the role of genetic variants in major depression" that are part of the Supplementary information of the article describing the study.</p> <p>The entry contains the following data:</p> <p><strong>Supplementary Tables S1-S7</strong></p> <p>Supplementary Table S1. Summary of resources.</p> <p>Supplementary Table S2. Causal GVs for MD.</p> <p>Supplementary Table S3. pGenes functional and disease enrichment analysis.</p> <p>Supplementary Table S4. Fine-mapped MD causal GVs disease enrichment analysis.</p> <p>Supplementary Table S5. Colocalizing GWAS-eQTLs association to disease.</p> <p>Supplementary Table S6. TFBS analysis.</p> <p>Supplementary Table S7. GVs state annotation. </p>
Data from: Integrative genomic analysis in African American children with asthma finds 3 novel loci associated with lung function
<p>Bronchodilator drugs are commonly prescribed for treatment and management of obstructive lung function present with diseases such as asthma. Administration of bronchodilator medication can partially or fully restore lung function as measured by pulmonary function tests. The genetics of baseline lung function measures taken prior to bronchodilator medication has been extensively studied, and the genetics of the bronchodilator response itself has received some attention. However, few studies have focused on the genetics of post-bronchodilator lung function. To address this gap, we analyzed lung function phenotypes in 1,103 subjects from the Study of African Americans, Asthma, Genes, and Environment (SAGE), a pediatric asthma case-control cohort, using an integrative genomic analysis approach that combined genotype, locus-specific genetic ancestry, and functional annotation information. We integrated genome-wide association study (GWAS) results with an admixture mapping scan of three pulmonary function tests (FEV1, FVC, and FEV1/FVC) taken before and after albuterol bronchodilator administration on the same subjects, yielding six traits. We identified 18 GWAS loci, and 5 additional loci from admixture mapping, spanning several known and novel lung function candidate genes. Most loci identified via admixture mapping exhibited wide variation in minor allele frequency across genotyped global populations. Functional fine-mapping revealed an enrichment of epigenetic annotations from peripheral blood mononuclear cells, fetal lung tissue, and lung fibroblasts. Our results point to three novel potential genetic drivers of pre- and post-bronchodilator lung function: ADAMTS1, RAD54B, and EGLN3. </p>
Identification and analysis of functional associations among natural eukaryotic genome editing components
<p>The contents of the data files for the manuscript "Identification and analysis of functional associations among natural eukaryotic genome editing components" are described below.</p> <p>Dataset 1 - ies_retention.tab<br> = All IES retention scores used in the manuscript</p> <p>Dataset 2 - oes_retention.tab<br> = OES retention estimates.</p> <p>Supplementary Data S1 - ies_retention_score_correlation_stats_all.txt<br> = Statistics for Spearman's correlations for all IESs.</p> <p>Supplementary Data S2 - ies_retention_score_correlation_stats_len_le_35bp.txt<br> = Statistics for Spearman's correlations for IESs <= 35 bp.</p> <p>Supplementary Data S3 - ies_retention_score_correlation_stats_len_ge_500bp.txt<br> = Statistics for Spearman's correlations for IESs >= 500 bp.</p> <p>Supplementary Data S4 - oes_retention_score_correlation_stats_all.txt<br> = Statistics for Spearman's correlations for OESs (>= 300 bp and 3x-70x PGM-KD<br> coverage).</p> <p>Supplementary Data S5 - ies_retention_score_correlation.comparison_stats.txt<br> = Statistics for comparisons of Spearman correlation differences for all IESs.</p> <p>Supplementary Data S6 - oes_retention_score_correlation.comparison_stats.txt<br> = Statistics for comparisons of Spearman correlation differences for all OESs.</p> <p>Supplementary Data S7 - ies_vs_oes_retention_score_correlation.comparisons_stats.txt<br> = Statistics for comparisons of the differences in Spearman correlations<br> between IESs and OESs.</p> <p>Supplementary Data S8 - OES.v1.fa<br> = OES sequences.</p> <p> </p>
Data from: Integrative genomic analysis in African American children with asthma finds 3 novel loci associated with lung function
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Analysis of fungal genomes reveals commonalities of intron gain or loss and functions in intron-poor species
<p>Datasets for DOI: <a href="https://doi.org/10.1101/2020.08.11.247098">10.1101/2020.08.11.247098</a>. Jupyter notebooks to reproduce the analysis of this study is available at <a href="https://github.com/Brookesloci/fungi_intron_paper_2020">GitHub</a></p> <ul> <li>annotations.total.txt.gz - gene annotation file of 350 fungi species and outgroups <em>Homo sapiens</em> and <em>Fonticula alba</em></li> <li>site_histories_41490_51_2L_1G.txt.gz - intron site histories of 263 fungi species and outgroups <em>Homo sapiens</em> and <em>Fonticula alba.</em></li> </ul>
Data from: Functional genomic analysis of corals from natural CO2-seeps reveals core molecular responses involved in acclimatization to ocean acidification
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Genome-wide analysis reveals extensive functional interaction between DNA replication initiation and transcription in the genome of Trypanosoma brucei
<p>Raw ChIP-chip and MFA-seq data from the paper listed above.</p>
Data from: Genome-wide association meta-analysis of functional outcome after ischemic stroke
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A functional map of genomic HIF1α-DNA complexes in the eye lens revealed through multiomics analysis [RNA-seq]
GEO Series GSE166632. Gallus gallus. 6 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide analysis of Musashi-2 targets reveals novel functions in governing epithelial cell migration
GEO Series GSE71333. Mus musculus. 17 samples. Type: Expression profiling by high throughput sequencing; Other.
Functional Genomic Analysis of Glaucoma Pathogenesis Due to gmds Mutation in Zebrafish
GEO Series GSE281042. Danio rerio. 12 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish [RNA-seq II]
GEO Series GSE120358. Procambarus virginalis. 3 samples. Type: Expression profiling by high throughput sequencing.
Whole genome expression analysis of a skin biopsy from an individual with multi-organ epithelial inflammation associated with an inherited loss-of-function mutation in EGFR
GEO Series GSE54162. Homo sapiens. 5 samples. Type: Expression profiling by array.
Comprehensive single cell transcriptomics analysis of murine osteosarcoma uncovers Skp2 function in metastasis, genomic instability and immune activation and reveals additional target pathways
GEO Series GSE262743. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
Integrated analysis of genome-wide profiling of lncRNA and mRNA expression and functional networks after botulinum toxin type A injection into submandibular gland of rats.
GEO Series GSE144985. Rattus norvegicus. 8 samples. Type: Non-coding RNA profiling by array; Expression profiling by array.
Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish
GEO Series GSE112411. Procambarus virginalis; Procambarus fallax. 26 samples. Type: Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [ChIP-Seq]
GEO Series GSE106372. Branchiostoma lanceolatum. 17 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Generation and functional analysis of defective viral genomes during SARS-CoV-2 infection
GEO Series GSE222381. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
Multiplexed functional genomic analysis of somatic 5’ untranslated region mutations across the spectrum of human prostate cancer (Exome-Seq)
GEO Series GSE174787. Homo sapiens. 10 samples. Type: Other.
Genome-wide analysis of PAPS1-dependent polyadenylation identifies novel roles for functionally specialized poly(A) polymerases in Arabidopsis thaliana
GEO Series GSE57690. Arabidopsis thaliana. 16 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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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.