RITAN: rapid integration of term annotation and network resources

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• High-throughput studies generate large gene sets requiring functional annotation.
• Current methods for gene set functional annotation are time-consuming and require bioinformatics expertise.
• Integrating data from disparate databases is a common, yet challenging, bioinformatics task.

Purpose of the Study:

• To develop an open-source R package for annotating gene sets with functions, pathways, and network interconnectivity.
• To streamline the integration of diverse biological databases for gene set analysis.
• To facilitate the interpretation of results from high-throughput biological experiments.

Main Methods:

• Developed an open-source R software package named RITAN (Rapid Integration of Term Annotation and Network resources).
• Integrated 16 term annotation resources (e.g., Gene Ontology, biologic pathways) and 9 network biology resources.
• Implemented tools for merging resources, exploring inter-resource relationships, and expanding gene sets using network neighbors.

Main Results:

• RITAN provides rapid and comprehensive annotation of gene lists using functional and network data.
• The package allows users to merge annotation resources, minimizing overlap and deriving novel combinations.
• Users can expand gene sets by identifying interacting genes from biological networks and subsequently identifying their functions.

Conclusions:

• RITAN effectively bridges high-throughput experimental results with functional annotation and network biology resources.
• The software package addresses the need for efficient integration of biological data.
• RITAN is available as an R package on GitHub and BioConductor.