التفاصيل البيبلوغرافية
| العنوان: |
DriverGenePathway: Identifying driver genes and driver pathways in cancer based on MutSigCV and statistical methods |
| المؤلفون: |
Xiaolu Xu, Zitong Qi, Dawei Zhang, Meiwei Zhang, Yonggong Ren, Zhaohong Geng |
| المصدر: |
Computational and Structural Biotechnology Journal, Vol 21, Iss , Pp 3124-3135 (2023) |
| بيانات النشر: |
Elsevier, 2023. |
| سنة النشر: |
2023 |
| المجموعة: |
LCC:Biotechnology |
| مصطلحات موضوعية: |
Cancer research, Driver gene, Driver pathway, MutSigCV, Statistical methods, Biotechnology, TP248.13-248.65 |
| الوصف: |
Although computational methods for driver gene identification have progressed rapidly, it is far from the goal of obtaining widely recognized driver genes for all cancer types. The driver gene lists predicted by these methods often lack consistency and stability across different studies or datasets. In addition to analytical performance, some tools may require further improvement regarding operability and system compatibility. Here, we developed a user-friendly R package (DriverGenePathway) integrating MutSigCV and statistical methods to identify cancer driver genes and pathways. The theoretical basis of the MutSigCV program is elaborated and integrated into DriverGenePathway, such as mutation categories discovery based on information entropy. Five methods of hypothesis testing, including the beta-binomial test, Fisher combined p-value test, likelihood ratio test, convolution test, and projection test, are used to identify the minimal core driver genes. Moreover, de novo methods, which can effectively overcome mutational heterogeneity, are introduced to identify driver pathways. Herein, we describe the computational structure and statistical fundamentals of the DriverGenePathway pipeline and demonstrate its performance using eight types of cancer from TCGA. DriverGenePathway correctly confirms many expected driver genes with high overlap with the Cancer Gene Census list and driver pathways associated with cancer development. The DriverGenePathway R package is freely available on GitHub: https://github.com/bioinformatics-xu/DriverGenePathway. |
| نوع الوثيقة: |
article |
| وصف الملف: |
electronic resource |
| اللغة: |
English |
| تدمد: |
2001-0370 |
| Relation: |
http://www.sciencedirect.com/science/article/pii/S2001037023002015; https://doaj.org/toc/2001-0370 |
| DOI: |
10.1016/j.csbj.2023.05.019 |
| URL الوصول: |
https://doaj.org/article/f8ce25a148d041a2bdafc776ae3713ba |
| رقم الانضمام: |
edsdoj.f8ce25a148d041a2bdafc776ae3713ba |
| قاعدة البيانات: |
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