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Updated: May 20, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

AraPath: a knowledgebase for pathway analysis in Arabidopsis.

Liming Lai¹, Arthur Liberzon, Jason Hennessey

¹Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57007, USA.

Bioinformatics (Oxford, England)

|July 5, 2012

Summary

Researchers created AraPath, a plant pathway knowledgebase, to interpret gene expression data. This database aids in generating testable hypotheses for plant molecular pathways from genomic studies.

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Last Updated: May 20, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

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Published on: October 17, 2017

Area of Science:

Plant genomics
Bioinformatics
Molecular biology

Background:

Interpreting plant genome-wide expression data is challenging due to limited pathway databases.
High-throughput genomics in plants is becoming standard practice.

Purpose of the Study:

To develop a comprehensive knowledgebase for plant pathway analysis.
To facilitate the interpretation of gene expression data in Arabidopsis.

Main Methods:

Compiled 1683 differentially expressed gene lists from 397 Arabidopsis gene-expression studies.
Integrated 1909 gene sets from Gene Ontology, KEGG, AraCyc, Plant Ontology, miRNA, transcription factors, and computational clusters.
Applied Gene Set Enrichment Analysis to cold acclimation expression data.

Main Results:

Created the AraPath database, a molecular signature database for Arabidopsis perturbations.
Successfully identified expected functional categories and pathways using Gene Set Enrichment Analysis.
Demonstrated the utility of AraPath for hypothesis generation.

Conclusions:

The AraPath database provides a valuable resource for plant pathway analysis.
It enables the generation of specific, testable hypotheses from plant gene expression data.
Facilitates a deeper understanding of molecular pathways in plants.