ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Pathway analysis methods aid hypothesis generation by mapping differentially expressed genes to reference pathways.
• Topological pathway analysis enhances specificity and sensitivity but often lacks accessible implementations.
• RNA-Seq technology is increasingly prevalent for gene expression profiling, necessitating robust analytical tools.

Purpose of the Study:

• To develop a comprehensive R/Bioconductor package for topology-based pathway analysis.
• To provide a uniform interface to multiple pathway analysis methods, including novel implementations.
• To facilitate the application of these methods across different species and data types.

Main Methods:

• Implementation of three novel topology-based pathway analysis methods.
• Adaptation of four existing topology-based pathway analysis methods.
• Development of functions for pathway and topology manipulation and visualization.

Main Results:

• The ToPASeq package offers a unified interface to seven distinct topology-based pathway analysis methods.
• The package supports the analysis of both microarray and RNA-Seq gene expression data.
• ToPASeq includes tailored visualization tools and facilitates cross-species pathway analysis.

Conclusions:

• ToPASeq is a novel R/Bioconductor package providing seven topology-based pathway analysis methods.
• The package is applicable to microarray and RNA-Seq data for various species.
• Integrated visualization tools enhance the interpretation of pathway analysis results.