Treffer: GenePioneer: a comprehensive Python package for identification of essential genes and modules in cancer.

Title:
GenePioneer: a comprehensive Python package for identification of essential genes and modules in cancer.
Authors:
Haerianardakani A; Department of Computer and Systems Sciences, Stockholm University, Stockholm 16455, Sweden., Taheri G; School of Electrical Engineering and Computer Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
Source:
Bioinformatics advances [Bioinform Adv] 2025 Apr 29; Vol. 5 (1), pp. vbaf094. Date of Electronic Publication: 2025 Apr 29 (Print Publication: 2025).
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9918282081306676 Publication Model: eCollection Cited Medium: Internet ISSN: 2635-0041 (Electronic) Linking ISSN: 26350041 NLM ISO Abbreviation: Bioinform Adv Subsets: PubMed not MEDLINE
Imprint Name(s):
Original Publication: [Oxford] : Oxford University Press : International Society for Computational Biology, [2021]-
References:
Comput Biol Med. 2024 Mar;171:108234. (PMID: 38430742)
Nature. 2014 Jan 23;505(7484):495-501. (PMID: 24390350)
Proc Natl Acad Sci U S A. 2010 Jan 19;107(3):961-8. (PMID: 20080596)
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515. (PMID: 30395287)
Appl Soft Comput. 2022 Oct;128:109510. (PMID: 35992221)
Nature. 2008 Oct 23;455(7216):1061-8. (PMID: 18772890)
Nucleic Acids Res. 2019 Jan 8;47(D1):D330-D338. (PMID: 30395331)
PLoS Comput Biol. 2022 Oct 17;18(10):e1010332. (PMID: 36251702)
Nat Rev Clin Oncol. 2018 Feb;15(2):81-94. (PMID: 29115304)
Nucleic Acids Res. 2016 Jan 4;44(D1):D457-62. (PMID: 26476454)
Entry Date(s):
Date Created: 20250526 Latest Revision: 20250621
Update Code:
20250621
PubMed Central ID:
PMC12098931
DOI:
10.1093/bioadv/vbaf094
PMID:
40417653
Database:
MEDLINE

Weitere Informationen

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.
Availability and Implementation: GenePioneer is released as an open-source software under the MIT license. The source code is available on GitHub at https://github.com/Golnazthr/ModuleDetection.
(© The Author(s) 2025. Published by Oxford University Press.)

None declared.