Location: Corn Host Plant Resistance ResearchTitle: A pathway association study tool for GWAS analyses of metabolic pathway information
|THRASH, ADAM - Mississippi State University|
Submitted to: The Journal of Visualized Experiments (JoVE)
Publication Type: Other
Publication Acceptance Date: 5/14/2020
Publication Date: 7/1/2020
Citation: Thrash, A., Warburton, M.L. 2020. A pathway association study tool for GWAS analyses of metabolic pathway information. The Journal of Visualized Experiments (JoVE). 161:e61268. https://doi.org/10.3791/61268.
Interpretive Summary: This is a video presentation of how our new computer program, PAST (Pathway Association Study Tool), is run. Adam Thrash shows potential users how to download the program, format and load data sets, choose the correct options in the tool, and run the analysis. We give tips on how to interpret the results. The video will be available online.
Technical Abstract: Recently, a new implementation of a previously described method for interpreting genome-wide association study (GWAS) data using metabolic pathway analysis has been developed and released. PAST (Pathway Association Study Tool) was developed to address concerns with user-friendliness and slow-running analyses. This new user-friendly tool has been released on Bioconductor and Github. In testing, PAST ran analyses in less than one hour that previously required twenty-four or more hours. In this paper/video, we present the protocol for using either the Shiny application or the R console to run PAST.