Knx Association Catalog Download
Basa Benejan
Epigenome-wide association studies (EWAS) seek to quantify associations between traits/exposures and DNA methylation measured at thousands or millions of CpG sites across the genome. In recent years, the increase in availability of DNA methylation measures in population-based cohorts and case-control studies has resulted in a dramatic expansion of the number of EWAS being performed and published. To make this rich source of results more accessible, we have manually curated a database of CpG-trait associations (with p
The White House Historical Association today released its annual holiday catalog featuring a wide range of holiday gifts, along with the beloved Official 2022 White House Ornament. The new items and ornament are available for purchase online through an interactive digital catalog and in stores.
Update (5/12/15): The NHGRI-EBI GWAS Catalog has moved to the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) at Users may now find the new search interface and updated content at this site. Questions about the GWAS Catalog may be directed to gwas...@ebi.ac.uk.
Why has the catalog moved to EMBL-EBI?
From September 2010 to the present, delivery and development of the Catalog has been a collaborative project between EMBL-EBI and NHGRI. In March 2015 the Catalog infrastructure moved to EMBL-EBI to enable delivery of an improved user interface, including ontology driven Catalog searching, and new curatorial infrastructure, supporting improved QC processes. Catalog content available through this original GWAS Catalog website was last updated on February 20th 2015 with all previous and updated content available at EMBL-EBI.
The genome-wide association study (GWAS) publications in the Catalog include a primary GWAS analysis, defined as array-based genotyping and analysis of 100,000+ pre-QC SNPs selected to tag variation across the genome and without regard to gene content. GWAS data from published studies which are incorporated into new GWAS analyses are eligible, provided they meet the other criteria. Studies imputing sequencing data to genotyping arrays are eligible as long as the arrays include sufficient genome-wide coverage so that the post-imputation analysis meets the definition of a GWAS analysis, as described above. The scope of the GWAS Catalog is currently being expanded to include studies of large-scale targeted/non-genome-wide arrays, including the Metabochip, Immunochip and Exome arrays. This is currently in a pilot phase where prioritization of targeted and exome array studies for inclusion in the Catalog is by 1) relevance of the trait analyzed 2) user request.
How to cite the NHGRI GWAS Catalog:
MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington Z, Welter D, Burdett T, Hindorff L, Flicek P, Cunningham F, and Parkinson H. The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). Nucleic Acids Research, 2017, Vol. 45 (Database issue): D896-D901.
The GWAS Catalog (www.ebi.ac.uk/gwas; 6) is a publicly available, manually curated resource of all published GWAS and association results, collaboratively produced and developed by the NHGRI and EMBL-EBI. It includes all eligible GWAS studies since the first published GWAS on age-related macular degeneration in 2005 (7). As of 1st September 2016 it contains 24,218 unique SNP-trait associations from 2,518 publications in 337 different journals. The Catalog summarizes a large body of diverse and unstructured data from the literature in an accessible, expertly curated and quality controlled resource. Catalog data are used by biologists, bioinformaticians and clinical/translational researchers as a starting point for further investigations to identify causal variants, understand disease mechanisms, and establish targets for novel therapies. Examples of such work include the analysis of Catalog data for identification of other traits associated with type 1 diabetes loci by Onengut-Gumuscu et al. (8); for evidence of pleiotropy by Sivakumaran et al. (9); for loci associated with seven common diseases to identify possible causal missense variants by Pal and Moult, 2015 (10); and for identification of new targets for known drugs by Mullen et al. (11). GWAS Catalog data are also integrated into many bioinformatics resources including Ensembl (12), the UCSC Genome Browser (13), PheGenI (14), HuGE Navigator (15) and GWASdb (16).
For inclusion in the Catalog, studies and associations must meet strict criteria (www.ebi.ac.uk/gwas/docs/methods); studies must include an array-based GWAS and analysis of >100 000 SNPs with genome-wide coverage, while SNP-trait associations must have a P-value
Search results are displayed in an interactive graphical user interface with improved data visualization, interrogation and integration with data from external resources. Results are displayed in tabular format, organized into separate facets for studies, associations and traits. Search results can be filtered, by P-value, odds ratio, beta coefficient, study date, reported trait, are sortable and can be downloaded in tab-delimited format. Links are available to relevant data in external resources, including the publication entry in Europe PMC (21), variant, genomic location and gene in Ensembl (12), and mapped ontology trait in EFO (17) enabling users to access additional information easily.
The GWAS Catalog's complete data in tab-delimited format (www.ebi.ac.uk/gwas/docs/downloads) is primarily used by bioinformaticians for bulk data access, allowing large-scale analysis of the data, annotation with additional data or integration into resources, e.g. Ensembl. We have expanded the range of download files available, with separate files for all associations and all studies, both with and without ontology mappings, and for ancestry data. We retained the original file format for association data, including all column headings, in order to provide backwards compatibility for programmatic parsing of the data. Studies are now included in a separate spreadsheet which provides a full list of all studies with a count of how many associations were identified for each study. We also provide a dedicated mapping spreadsheet between all reported GWAS Catalog traits and ontology terms, along with the GWAS diagram trait category. This allows users to identify the child terms included under each higher-level trait category on the GWAS diagram for example congenital heart disease is a cardiovascular disease.
GWAS study design, genotyping technologies and user needs have advanced since the initial design of the Catalog. It is essential that the Catalog adapts to contain the most relevant and up-to-date studies and association results. Studies using large-scale targeted/non-genome-wide arrays, including the Metabochip, Immunochip and Exome arrays, and genotyping by sequencing are currently not included in the Catalog. Following feedback from our users we have plans to extend the scope of the Catalog to include all large-scale association studies and all SNP-trait associations, regardless of P-value. This, coupled with programmatic access, will vastly improve the utility of the Catalog for large-scale meta-analyses of published GWAS data with increased power to identify causal loci.
In response to this issue the WHO has developed a catalogue of Mtb mutations in the and their association with phenotypic drug resistance. The catalogue provides a reference standard for the interpretation of mutations conferring resistance to all first-line and a variety of second-line drugs. The report summarises the analysis of over 38,000 isolates with matched data on whole genome sequencing and phenotypic drug susceptibility testing from over 40 countries for 13 anti-TB medicines. It lists over 17,000 mutations, their frequency and association with or not with resistance and includes methods used, mutations identified and summaries of important findings for each drug.
Tuberculosis laboratories around the world can use the catalogue as a support in the interpretation of genome sequencing results. The catalogue can also guide the development of new molecular drug susceptibility tests, including next-generation sequencing.
If you are willing and able, please consider contributing today! Items you'll find in the catalog include general, open ended donations to either organization; the ability to sponsor the student registration fee ($20) or student registration fee to the Annual Convention ($35), and the ability to contribute towards the WPF's scholarship program.
Published epigenome-wide association studies are identified through periodic PubMed searches using the journalclub R package. The search terms are "epigenome-wide" OR "epigenome wide" OR "EWAS" OR "genome-wide AND methylation" OR "genome wide AND methylation". There are also restrictions placed on the year of publication (i.e. studies after 2010) and whether the study is in human samples.
On the screen a table of results is presented with a subset of columns (or variables) to browse. The full dataset with all variables for the query is available to download. This file is a tab-deliminated tsv file with the same variables as in the downloadable catalog.
AGMA has helped to set national gearing standards since 1916. The association also serves as the focal point within the United States for the development of ISO gearing standards.
Today, this work is carried out by 23 Technical Committees. AGMA standards address nearly all the critical gearing topics, from load capacity and lubrication to accuracy and inspection.
The catalog includes information from Denmark, EU, France, Germany, Netherlands, South Africa, South Korea, Sweden, and UK. It covers recyclability evaluations for rigid PET, rigid HDPE, rigid PP, and flexible PE film packaging.
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