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GenePioneer: A comprehensive Python package for identification of essential genes and modules in cancer
Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
Number of Authors: 22025 (English)In: Bioinformatics Advances, E-ISSN 2635-0041, Vol. 5, no 1, article id vbaf094Article in journal (Refereed) Published
Abstract [en]

Summary: We propose a network-based unsupervised learning model to identify essential cancer genes and modules for 12 different cancer types, supported by a Python package for practical application. The model constructs a gene network from frequently mutated genes and biological processes, ranks genes using topological features, and detects critical modules. Evaluation across cancer types confirms its effectiveness in prioritizing cancer-related genes and uncovering relevant modules. The Python package allows users to input gene lists, retrieve rankings, and identify associated modules. This work provides a robust method for gene prioritization and module detection, along with a user-friendly package to support research and clinical decision-making in cancer genomics.

Place, publisher, year, edition, pages
2025. Vol. 5, no 1, article id vbaf094
National Category
Medical Genetics and Genomics
Identifiers
URN: urn:nbn:se:su:diva-244104DOI: 10.1093/bioadv/vbaf094ISI: 001492858700001Scopus ID: 2-s2.0-105006519499OAI: oai:DiVA.org:su-244104DiVA, id: diva2:1967918
Available from: 2025-06-12 Created: 2025-06-12 Last updated: 2026-01-29Bibliographically approved

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