Genome-wide association studies in Arabidopsis thaliana

Background

The GWA results presented here are described in a paper that is currently under consideration for publication: "Genome-wide association study of 107 phenotypes in a common set of Arabidopsis thaliana inbred lines", by S. Atwell et al.  This page is supposed to remain hidden until the paper is accepted.  If you are not an author, or involved with the review of the paper, you probably should not be looking at this.  However, since you are here, feel free to look around.  Just remember to treat the data and results as if you were a reviewer: keep them confidential, and do not use them in your own research.  In general, we are in favor of as much openness as possible, and would like our database to grow by adding other results to it.  The Arabidopsis community has a always been good at cooperating and sharing data, and we would like to continue this tradition.  The flip-side of this is respecting the work of others.

The 250k SNP project is a collaboration between the groups of  Joy Bergelson, Justin Borevitz, and Magnus Nordborg, but many people at many institutions contributed to the results presented here.  Please see the paper for details.  The display of the data is mainly due to Yu Huang, a graduate students in the Nordborg group.  Another student, Dazhe Meng, did the GBrowse section.

About the website

The main interface to the data is here.  It lists all phenotypes.  Clicking on one brings up a window with three tabs: one that provides summary information about the results for this phenotype, and two GWA plots.  Individual points in these plots are clickable, and give you detailed information about the SNP in question.  Try it!

A second interface allows you to search for associations by gene name instead of looking at the genome-wide results.  Find out what your favorite gene is doing by clicking here!