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Madison, WI 53726-2398
Phone: (608) 231-9200
Fax: (608) 231-9592


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Title: PAST: The Pathway Association Studies Tool to Infer Biological Meaning from GWAS Datasets

Source: Plants

Author(s)Thrash, Adam ; Tang, Juliet D.; DeOrnellis, Mason ; Peterson, Daniel G.; Warburton, Marilyn L.

Publication Year: 2020  View PDF »

Category: Journal Articles
Associated Research Project(s):   FPL-4723-3A

Abstract: In recent years, a bioinformatics method for interpreting genome-wide association study (GWAS) data using metabolic pathway analysis has been developed and successfully used to fnd signifcant pathways and mechanisms explaining phenotypic traits of interest in plants. However, the many scripts implementing this method were not straightforward to use, had to be customized for each project, required user supervision, and took more than 24 h to process data. PAST (Pathway Association Study Tool), a new implementation of this method, has been developed to address these concerns. PAST has been implemented as a package for the R language. Two user-interfaces are provided; PAST can be run by loading the package in R and calling its methods, or by using an R Shiny guided user interface. In testing, PAST completed analyses in approximately half an hour to one hour by processing data in parallel and produced the same results as the previously developed method. PAST has many user-specifed options for maximum customization. Thus, to promote a powerful new pathway analysis methodology that interprets GWAS data to fnd biological mechanisms associated with traits of interest, we developed a more accessible, efficient, and user-friendly tool. These attributes make PAST accessible to researchers interested in associating metabolic pathways with GWAS datasets to better understand the genetic architecture and mechanisms affecting phenotypes.

Keywords: metabolic pathway analysis; genome-wide association study (GWAS); maize (Zea mays L.)

Publication Review Process: Formally Refereed

File size: 1,024 kb(s)

Date posted: 03/16/2020

This publication is also viewable on Treesearch:  view
RITS Product ID: 97321
Current FPL Scientist associated with this product
Tang, Juliet
Research Forest Products Technologist

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