The R implementation of the CRAN package PATHChange, a tool to study genetic pathway alterations in transcriptomic...

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Interpreting large-scale transcriptomic data is crucial for biological discovery.
• Identifying differential pathway expression aids in understanding complex biological systems.
• Existing tools may not be optimized for specific comparative analyses with control groups.

Purpose of the Study:

• To introduce PATHChange, a novel statistical R package.
• To facilitate the analysis of differential pathway expression from transcriptomic data.
• To provide a user-friendly tool for researchers working with Gene Expression Omnibus (GEO) datasets.

Main Methods:

• PATHChange is a statistical package implemented in R.
• It processes data downloaded from the Gene Expression Omnibus (GEO) database.
• The package is designed for comparative studies, including those with control samples.

Main Results:

• PATHChange enables the determination of differential pathway expression.
• The package integrates seamlessly with GEO data.
• Demonstrates utility through a practical example of its implementation.

Conclusions:

• PATHChange offers a valuable tool for transcriptomic data analysis.
• It enhances the interpretation of biological studies by focusing on pathway alterations.
• The package supports robust comparative analyses in systems biology research.