Pathway Regulation Score (PRS) Tool

PRS tool is a MATLAB based graphical user interface that helps researchers analyse their datasets using the proposed PRS method and KEGG pathway database.


The interface provides users with several functions:

  • Analysis of a microarray gene expression dataset using two different scores, PRS and z-score. The end-user needs to specify the type of species (the package currently supports three species only: human, mouse, and rat) and the type of pathways (signalling or metabolic) then upload the raw data file. The output of the analysis is two lists of pathways ranked using different scores (PRS, z-score).
  • Normalisation and evaluation of PRS values using a non-parametric permutation method.
  • Retrieval of a pre-analysed dataset (these are stored in .mat format).
  • Other options include: browsing and visualising pathway map enriched with a given dataset.

If you used the tool please cite the following article: Ibrahim, M., S. Jassim, M. Cawthorne & K. Langlands, “A topology-based score for pathway enrichment”, Journal of Computational Biology 19.5 (May 2012), 563-573

An abstract of the article is available in the Journal of Computational Biology website.

A copy of the software used to generate the results can be downloaded here: Topology-based Pathway Analysis Tool

Required Products: MATLAB

MATLAB release: MATLAB 7.9.0 (R2009b)