RamiGO

RamiGO provides an R/Bioconductor interface to AmiGO for visualization and analysis of Gene Ontology (GO) trees and gene-set results.

Key Features:

• R/Bioconductor package: Implemented as an R/Bioconductor package for analysis within the R environment.
• Integration with AmiGO: Connects to the AmiGO API to retrieve and visualize GO terms.
• Graphviz-DOT import: Imports Graphviz-DOT format files into R for GO graph representation.
• Visualization export: Exports visualizations as SVG or PNG and exports graph data to Cytoscape for network analysis.
• Customization and highlighting: Supports annotation customization and highlighting of specific GO terms.
• P-value color-coding: Allows color-coding of GO terms based on P-values.
• Simplified summary trees: Generates simplified summary GO trees to reduce complexity.
• License and requirements: Released under the Artistic-2.0 License and requires R version 2.15.0 or higher.

Scientific Applications:

• Genome-wide gene set analyses: Used for genome-wide gene set analyses to identify enriched GO terms and pathways.
• Breast cancer prognostic gene analysis: Applied to analysis of prognostic genes in breast cancer to identify relevant biological pathways and processes.

Methodology:

Connects to the AmiGO API, imports Graphviz-DOT files into R, produces GO tree visualizations exportable as SVG/PNG or to Cytoscape, supports annotation-based highlighting and P-value color-coding, and generates simplified summary GO trees.