agriGO

agriGO performs gene ontology (GO) analyses tailored for agricultural research.

Key Features:

• Expanded Organism and Gene Identifier Support: Supports 38 agricultural species across 274 data types for broad coverage of agricultural gene sets.
• Flexible User Input: Accepts user-defined reference datasets and annotations for customized analyses.
• Gene Set Enrichment Strategies: Incorporates Gene Set Enrichment Analysis (GSEA) alongside enrichment approaches for functional interpretation.
• Integrated Analysis Tools: Provides SEA (Singular Enrichment Analysis), PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (transfer of gene identifiers by BLAST), and SEACOMPARE (cross comparison of SEA).
• Cross-Comparison and Visualization: Enables comparative analysis across multiple datasets and visualization of comparative enrichment results.
• GO Data Repository: Serves as a repository for GO data with search and download functionality.

Scientific Applications:

• Functional Annotation: Assigns and interprets GO terms for gene sets derived from high-throughput experiments.
• Enrichment Analysis: Detects over-represented GO categories using SEA, PAGE, and GSEA methodologies.
• Comparative Genomics: Facilitates cross-species and cross-dataset comparisons of GO enrichment, including ID transfer via BLAST4ID.
• Agricultural and Plant Research: Supports studies in plant biology, crop improvement, and sustainable agriculture by enabling cross-species functional exploration.

Methodology:

Performs GO analyses using SEA, PAGE, and GSEA; transfers gene identifiers via BLAST4ID; performs cross-dataset comparison with SEACOMPARE; accepts user-defined reference datasets and annotations and provides GO data search and download.