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ARS Home » Southeast Area » Mississippi State, Mississippi » Crop Science Research Laboratory » Corn Host Plant Resistance Research » Research » Publications at this Location » Publication #371674
Research Project: Enhanced Resistance of Maize to Aspergillus flavus Infection, Aflatoxin Accumulation, and Insect Damage

Location: Corn Host Plant Resistance Research

Title: A pathway association study tool for GWAS analyses of metabolic pathway information

Author
item THRASH, ADAM - Mississippi State University
item Warburton, Marilyn

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.
DOI: 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.