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Updated: Jun 2, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

The PathOlogist: an automated tool for pathway-centric analysis.

Sharon I Greenblum¹, Sol Efroni, Carl F Schaefer

¹Department of Genome Sciences, University of Washington, Seattle WA, USA. sharongreenblum@gmail.com

BMC Bioinformatics

|May 6, 2011

Summary

This summary is machine-generated.

The PathOlogist tool quantifies pathway behavior from gene expression data, offering a robust alternative to single-gene analysis. It identifies altered biological pathways in disease, aiding in treatment response differentiation.

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Area of Science:

Bioinformatics
Systems Biology
Computational Biology

Background:

The PathOlogist tool transforms gene expression data into quantitative pathway-level descriptors.
It offers a robust alternative to single-gene-to-phenotype association studies by considering molecular interaction complexity.

Purpose of the Study:

To present a novel computational tool, The PathOlogist, for analyzing pathway behavior.
To enable the identification of functional processes altered in disease states.

Main Methods:

Calculates pathway 'activity' and 'consistency' metrics using molecular abundance data for over 500 canonical pathways.
Integrates visualization of pathway components, hierarchical clustering, and statistical analyses to link pathway behavior with clinical features.

Main Results:

Demonstrates the utility of The PathOlogist in establishing pathway signatures.
Successfully differentiates breast cancer cell lines based on treatment response using pathway signatures.

Conclusions:

The PathOlogist facilitates the identification of altered functional processes in disease, moving beyond individual molecule analysis.
Provides accessible statistical power and biological significance for researchers and analysts.
Highlights the tool's capability in differentiating cell lines by treatment response through pathway signatures.