PlantGSEA

PlantGSEA performs gene set enrichment analysis for plant species, enabling interpretation of large-scale genomic data using predefined gene sets and Gene Ontology (GO) annotations.

Key Features:

• Extensive Gene Set Collection: Incorporates 20,290 defined gene sets sourced from various databases to support detailed enrichment analysis.
• Support for Multiple Species and Identifiers: Supports gene locus IDs and Affymatrix microarray probe set IDs for Arabidopsis thaliana, Oryza sativa (rice), Zea mays (maize), and Gossypium raimondii.
• Integration with Established Tools: Builds on methodologies and resources from EasyGO and agriGO developed by the same laboratory.

Scientific Applications:

• Functional interpretation of plant genomic data: Provides enrichment results that inform biological processes, molecular functions, and cellular components via GO annotations.
• Studies of development, stress responses, and metabolism: Aids hypothesis generation and validation in investigations of plant development, stress responses, and metabolic pathways.

Methodology:

Uses the GSEA approach by ranking genes according to their correlation with a phenotype or condition and assessing whether predefined gene sets show statistically significant differences between phenotypic states, with emphasis on plant-specific datasets and identifiers.