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Nucleic Acids Res. 2018 Jan 4;46(D1):D1150-D1156. doi: 10.1093/nar/gkx954.

The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog.

Author information

1
Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.
2
Swiss Institute of Bioinformatics, 4056 Basel, Switzerland.
3
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria.
4
Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90007, USA.
5
Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
6
Center for Computational and Theoretical Biology, University Würzburg, 97074 Würzburg, Germany.

Abstract

The abundance of high-quality genotype and phenotype data for the model organism Arabidopsis thaliana enables scientists to study the genetic architecture of many complex traits at an unprecedented level of detail using genome-wide association studies (GWAS). GWAS have been a great success in A. thaliana and many SNP-trait associations have been published. With the AraGWAS Catalog (https://aragwas.1001genomes.org) we provide a publicly available, manually curated and standardized GWAS catalog for all publicly available phenotypes from the central A. thaliana phenotype repository, AraPheno. All GWAS have been recomputed on the latest imputed genotype release of the 1001 Genomes Consortium using a standardized GWAS pipeline to ensure comparability between results. The catalog includes currently 167 phenotypes and more than 222 000 SNP-trait associations with P < 10-4, of which 3887 are significantly associated using permutation-based thresholds. The AraGWAS Catalog can be accessed via a modern web-interface and provides various features to easily access, download and visualize the results and summary statistics across GWAS.

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