ROntoTools

ROntoTools performs topology-based pathway analysis to identify and interpret signaling pathways impacted by phenotypes using full transcriptomic measurements from next-generation sequencing (NGS).

Key Features:

• Topology-Based Pathway Analysis: Employs a topology-based approach that distinguishes primary gene deregulation from upstream or downstream signaling effects.
• Comprehensive Data Utilization: Incorporates the entire set of transcriptomic measurements rather than restricting analysis to differentially expressed genes, avoiding the loss of over 99% of collected data in typical workflows.
• Improved Accuracy and Reliability: Demonstrates improved performance in comparative analyses versus SPIA, GSEA, and GSA across 24 human disease datasets (12 conditions) and 8 yeast knock-out datasets.
• Integration with R/Bioconductor: Implemented in the R programming language and distributed as a Bioconductor package (versions ≥ 2.0.0).

Scientific Applications:

• Disease Mechanism Elucidation: Identifies signaling pathways that contribute to human disease phenotypes.
• Phenotype Analysis: Maps gene expression changes to biological pathways to investigate the genetic basis of phenotypes.
• Genomic Research: Enhances interpretation of whole-genome and large-scale transcriptomic experiments derived from NGS.

Methodology:

Applies topology-based algorithms that consider both primary deregulation and downstream signaling effects to analyze full transcriptomic measurements from NGS.