Banner for LabNotes
From Lab Notes
Contact Information
Forest Products Laboratory
One Gifford Pinchot Drive
Madison, WI 53726-2398
Phone: (608) 231-9200
Fax: (608) 231-9592
Email

 

You are here: FPL Home  / Information Products & Services  / Publications

Requested Product

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
  

Additional items that might interest you
View the video celebrating FPL's 100 years of public service in 2010, from the producers of the Greatest Good....view

Research Highlights from FPL....view

Termite Eradication: A search for the Holy Grail.... view

Moisture Management in Residential Construction Series videos...view

Wood Floor Systems in Residential Construction Series videos....view
- FPL's Mission and Strategic Plan -

FPL's mission is to identify and conduct innovative wood and fiber utilization research that contributes to conservation and productivity of the forest resource, thereby sustaining forests, the economy, and quality of life. ... ..more »

- FPL Research Emphasis Areas -
Advanced Composites

As an integral part of the FPL mission, we improve the long-term sustainability of our Nation's forests by creating valuable composite products from biobased materials ... ..more »


Advanced Structures

The FPL has been in the forefront of wood-frame housing research since 1910 and has long been recognized as a world leader in such housing-related areas as engineered wood ... ..more »


Forest Biorefinery

We all know the compelling reasons that the United States needs to reduce its dependence on fossil fuels. Historically, the greatest increases in energy demand have been for transportation fuels ... ..more »


Nanotechnology

A leader in wood products research for over a century, the FPL is positioning itself to become the lead Federal research facility for the application of nanotechnology in forest products ... more »


Woody Biomass Utilization

Forests in the United States contain a substantial amount of small-diameter, overstocked, and underutilized material.FPL research projects are exploring the potential of the small-diameter ... ..more »