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A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

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Published on: July 1, 2020

AgBase: a functional genomics resource for agriculture.

Fiona M McCarthy¹, Nan Wang, G Bryce Magee

¹Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA. fmccarthy@cvm.msstate.edu

|September 12, 2006

Summary

AgBase is a new resource providing functional genomics and systems biology tools for agricultural species. It improves genome annotation and aids research in agriculture, human health, and evolutionary biology.

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Area of Science:

Genomics
Systems Biology
Bioinformatics

Background:

Agricultural species genomes are poorly annotated, hindering systems biology research.
Limited funding and smaller research communities impact agricultural genomics.
Agricultural microorganisms can be human zoonoses, necessitating better annotation.

Purpose of the Study:

To establish AgBase, a public resource for agricultural genome annotation.
To facilitate systems biology in agriculturally important species.
To provide computational tools for functional genomics data analysis.

Main Methods:

Developed AgBase, a curated, web-accessible database.
Utilized standardized nomenclature and Gene Ontology (GO) for annotation.
Created computational tools for batch processing, ortholog identification, and proteomics analysis.

Main Results:

AgBase offers structural and functional annotation for agricultural genomes.
Tools facilitate analysis of GO annotations, orthologs, and proteomics data.
A journal database prevents redundant manual GO curation.

Conclusions:

AgBase is the first database for functional genomics in agricultural species.
It improves genome annotation using experimental data and functional characterization.
The resource and tools are applicable to diverse fields and other species.