PAST (Pathway Association Study Tool) at MaizeGDB

About PAST

PAST: the Pathway Association Study Tool assigns your SNPs to genes and your genes to metabolic pathways. PAST transfers the attributes of your SNPs (R2, p) to the genes and identifies pathways that are significantly associated with your trait of interest.

By running PAST, either through the Shiny application or through the R console, researchers can gain a deeper understanding of the biological meaning of their GWAS results by investigating the metabolic pathways involved.

A screen capture of the PAST output.

How to run PAST at MaizeGDB

MaizeGDB has three instances of PAST installed on R Shiny servers. There is a limit to running one job per server. If a link is unresponsive, please try a different server or check back later when the server becomes available. An average job takes between 30 - 90 minutes to complete.

MaizeGD PAST server #1
MaizeGD PAST server #2
MaizeGD PAST server #3

How to run PAST on a local machine

The best way to run past is to install it locally by either using Docker or running it through Bioconductor.

PAST on Bioconductor
GitHub repository
app.R file

Docker Instructions

Pre-requisite step:

1) Install Docker on your computer.

Simple steps:

1) Open a terminal and type the command:

$ docker run -it -d -p 80:3838 --name past maizegdb/past

2) Open a web browser and navigate to http://localhost.

Helpful docker commands:

The docker container will continue to run on your local machine until you tell it to stop with this command:

$ docker stop past

To check whether any containers are still running use this command:

$ docker ps

Documentation and sample data

Citations using PAST methodology:

  • Li et al. 2019. Leveraging GWAS data to identify metabolic pathways and networks involved in maize lipid biosynthesis. Plant J, 98:853-863
  • Warburton et al. 2017. Genome-wide association and metabolic pathway analysis of corn earworm resistance in maize. TPG: doi: 11:170069.
  • Tang et al. 2015. Using genome-wide associations to identify metabolic pathways involved in maize aflatoxin accumulation resistance. BMC Genomics 16:673.