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Updated: May 22, 2026
10:13
A Multiplexed Luciferase-based Screening Platform for Interrogating Cancer-associated Signal Transduction in Cultured Cells
Published on: July 3, 2013
Sensitive detection of pathway perturbations in cancers
Corban G Rivera1, Brett M Tyler, T M Murali
1Department of Computer Science, Virginia Tech, Blacksburg, VA, USA.
BMC Bioinformatics
|April 28, 2012
Summary
This study introduces a computational method to identify perturbed pathways in cancer by analyzing gene expression data and molecular interactions. The approach pinpoints specific sub-pathways, offering more sensitive and robust cancer pathway analysis.
Area of Science:
- Computational Biology
- Systems Biology
- Genomics
Background:
- Cellular function relies on complex molecular interaction networks.
- Linking diseases to pathway perturbations can reveal disease mechanisms and treatment responses.
Purpose of the Study:
- To develop a computational method for detecting pathway perturbations in cancer.
- To improve upon existing methods by considering gene product interactions and focusing on sub-pathways.
Main Methods:
- Compared gene expression profiles from cancer and normal tissues.
- Utilized a scoring function that incorporates gene interactions within pathways.
- Identified and statistically assessed the significance of the most perturbed sub-pathway using permutation tests.
- Applied the method to pathways from the Netpath database and gene expression data from the Global Cancer Map.
Main Results:
- The method demonstrated higher sensitivity than approaches that ignore interactions or assess entire pathways.
- The approach is robust to minor variations in input data.
- Confirmed known associations between pathways and cancers.
- Identified specific, perturbed sub-pathways within broader pathways.
Conclusions:
- Integrating gene expression data with pathway interaction structures effectively detects cancer-associated perturbed pathways.
- Cancer-specific pathway perturbations may be partial, even in well-studied pathways.
- Further investigation of cancer-specific sub-pathways can elucidate cancer similarities and differences.
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