Oncofinder, a new method for the analysis of intracellular signaling pathway activation using transcriptomic data
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Updated: May 1, 2026
Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis
Published on: June 27, 2020
Anton A Buzdin1, Alex A Zhavoronkov2, Mikhail B Korzinkin3
1Pathway Pharmaceuticals, Limited Wan Chai, Hong Kong, Hong Kong ; D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology Moscow, Russia ; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Moscow, Russia ; Biological and Medical Physics, Moscow Institute of Physics and Technology Dolgoprudny, Russia.
Abstract:
We propose a new biomathematical method, OncoFinder, for both quantitative and qualitative analysis of the intracellular signaling pathway activation (SPA). This method is universal and may be used for the analysis of any physiological, stress, malignancy and other perturbed conditions at the molecular level. In contrast to the other existing techniques for aggregation and generalization of the gene expression data for individual samples, we suggest to distinguish the positive/activator and negative/repressor role of every gene product in each pathway. We show that the relative importance of each gene product in a pathway can be assessed using kinetic models for "low-level" protein interactions. Although the importance factors for the pathway members cannot be so far established for most of the signaling pathways due to the lack of the required experimental data, we showed that ignoring these factors can be sometimes acceptable and that the simplified formula for SPA evaluation may be applied for many cases. We hope that due to its universal applicability, the method OncoFinder will be widely used by the researcher community.
Insights
OncoFinder is a novel biomathematical method for analyzing intracellular signaling pathway activation (SPA). It distinguishes gene product roles and assesses their importance, offering a universal tool for various biological conditions.
Area of Science:
- Biomathematics
- Molecular Biology
- Systems Biology
Background:
- Intracellular signaling pathway activation (SPA) is crucial for understanding cellular responses.
- Existing methods for analyzing gene expression data have limitations in distinguishing gene product roles.
- Accurate assessment of SPA is vital for studying physiological, stress, and malignancy conditions.
Purpose of the Study:
- To introduce OncoFinder, a universal biomathematical method for quantitative and qualitative SPA analysis.
- To differentiate the positive/activator and negative/repressor roles of gene products within signaling pathways.
- To enable the assessment of individual gene product importance in pathway activation.
Main Methods:
- Development of a novel biomathematical approach, OncoFinder.
- Utilizing kinetic models to assess the relative importance of gene products based on protein interactions.
- Proposing a method to distinguish between positive and negative regulatory roles of genes in pathways.
Main Results:
- OncoFinder provides a universal framework for SPA analysis applicable to diverse biological states.
- The method accounts for the distinct roles (activator/repressor) of gene products.
- Simplified SPA evaluation formulas are applicable even when gene product importance factors are unknown.
Conclusions:
- OncoFinder offers a versatile and powerful tool for researchers studying signaling pathways.
- The method's ability to differentiate gene product roles enhances the accuracy of SPA analysis.
- Widespread adoption of OncoFinder is anticipated due to its broad applicability and potential to advance molecular-level research.
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