ToPASeq

ToPASeq performs topology-based pathway analysis of gene expression data from RNA-Seq and microarray technologies to assess pathway perturbations using pathway topology.

Key Features:

• Implementation: Implemented as an R/Bioconductor package.
• Topology-based methods: Implements seven topology-based pathway analysis methods including SPIA, DEGraph, TopologyGSA, TAPPA, PRS, and PWEA.
• Custom implementations: Contains three novel method implementations and four adaptations of existing methodologies within a unified framework.
• Visualization tools: Provides tailored visualization functions for interpreting and presenting pathway analysis results.
• Pathway import and manipulation: Offers tools to import and manipulate pathway definitions and topologies for multiple species.
• Comparative analysis: Supports comparison of differential expression between two conditions using both microarray and RNA-Seq data.

Scientific Applications:

• Hypothesis generation: Maps differentially expressed genes to reference pathways and assesses topology-aware enrichment to generate biologically relevant hypotheses.
• Pathway-level inference: Increases specificity and sensitivity of identifying perturbed biological processes by incorporating pathway topological structure.
• Cross-platform and cross-species analysis: Enables comparative pathway analysis across RNA-Seq and microarray platforms and across species when pathway topologies are provided.

Methodology:

Applies topology-based pathway analysis methods (SPIA, DEGraph, TopologyGSA, TAPPA, PRS, PWEA) by leveraging pathway topologies and mapping differentially expressed genes derived from RNA-Seq and microarray experiments.