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通过综合网络分析鉴定常见驱动基因模块及癌症之间的关联

Identification of Common Driver Gene Modules and Associations between Cancers through Integrated Network Analysis.

作者信息

Gao Bo, Zhao Yue, Gao Yonghang, Li Guojun, Wu Ling-Yun

机构信息

IAM MADIS NCMIS Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China.

School of Mathematics Shandong University Jinan 250100 China.

出版信息

Glob Chall. 2021 Jun 19;5(9):2100006. doi: 10.1002/gch2.202100006. eCollection 2021 Sep.

DOI:10.1002/gch2.202100006
PMID:34504716
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8414517/
Abstract

High-throughput biological data has created an unprecedented opportunity for illuminating the mechanisms of tumor emergence and evolution. An important and challenging problem in deciphering cancers is to investigate the commonalities of driver genes and pathways and the associations between cancers. Aiming at this problem, a tool ComCovEx is developed to identify common cancer driver gene modules between two cancers by searching for the candidates in local signaling networks using an exclusivity-coverage iteration strategy and outputting those with significant coverage and exclusivity for both cancers. The associations of the cancer pairs are further evaluated by Fisher's exact test. Being applied to 11 TCGA cancer datasets, ComCovEx identifies 13 significantly associated cancer pairs with plenty of biologically significant common gene modules. The novel results of cancer relationship and common gene modules reveal the relevant pathological basis of different cancer types and provide new clues to diagnosis and drug treatment in associated cancers.

摘要

高通量生物学数据为阐明肿瘤发生和演变机制创造了前所未有的机会。在解读癌症过程中，一个重要且具有挑战性的问题是研究驱动基因和信号通路的共性以及癌症之间的关联。针对这一问题，开发了一种工具ComCovEx，通过使用排他性-覆盖迭代策略在局部信号网络中搜索候选基因，来识别两种癌症之间的常见癌症驱动基因模块，并输出对两种癌症都具有显著覆盖度和排他性的模块。癌症对之间的关联通过Fisher精确检验进一步评估。将ComCovEx应用于11个TCGA癌症数据集时，它识别出13对显著相关的癌症对以及大量具有生物学意义的常见基因模块。癌症关系和常见基因模块的新结果揭示了不同癌症类型的相关病理基础，并为相关癌症的诊断和药物治疗提供了新线索。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/8414517/2e4110b73c64/GCH2-5-2100006-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/8414517/5dedca9a344f/GCH2-5-2100006-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/8414517/95befabf7445/GCH2-5-2100006-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/8414517/6e132b6974a8/GCH2-5-2100006-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/8414517/d0d9fbd65e92/GCH2-5-2100006-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/8414517/a94e71323141/GCH2-5-2100006-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/8414517/4ad4c7060e32/GCH2-5-2100006-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/8414517/2e4110b73c64/GCH2-5-2100006-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/8414517/5dedca9a344f/GCH2-5-2100006-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/8414517/95befabf7445/GCH2-5-2100006-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/8414517/6e132b6974a8/GCH2-5-2100006-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/8414517/d0d9fbd65e92/GCH2-5-2100006-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/8414517/a94e71323141/GCH2-5-2100006-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/8414517/4ad4c7060e32/GCH2-5-2100006-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9c1/8414517/2e4110b73c64/GCH2-5-2100006-g004.jpg

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本文引用的文献

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Brief Bioinform. 2021 May 20;22(3). doi: 10.1093/bib/bbaa119.
2
Simultaneous expression of TTF1 and GATA3 in a lung biopsy sample: confusion in diagnostic pathology.肺活检样本中TTF1和GATA3的同时表达：诊断病理学中的困惑
Int J Clin Exp Pathol. 2019 Sep 1;12(9):3613-3619. eCollection 2019.
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A systematic analysis of immune genes and overall survival in cancer patients.癌症患者免疫基因与总生存期的系统分析。
BMC Cancer. 2019 Dec 16;19(1):1225. doi: 10.1186/s12885-019-6414-6.
4
Myoferlin, a multifunctional protein in normal cells, has novel and key roles in various cancers.肌联蛋白是一种正常细胞中的多功能蛋白，在多种癌症中具有新颖而关键的作用。
J Cell Mol Med. 2019 Nov;23(11):7180-7189. doi: 10.1111/jcmm.14648. Epub 2019 Sep 1.
5
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets.Metascape 为系统水平数据集的分析提供了面向生物学家的资源。
Nat Commun. 2019 Apr 3;10(1):1523. doi: 10.1038/s41467-019-09234-6.
6
Prediction of Driver Modules via Balancing Exclusive Coverages of Mutations in Cancer Samples.通过平衡癌症样本中突变的排他性覆盖来预测驱动模块
Adv Sci (Weinh). 2018 Dec 18;6(4):1801384. doi: 10.1002/advs.201801384. eCollection 2019 Feb 20.
7
The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens.癌症基因网络（NCG）：从癌症测序筛选中已知和候选癌症基因的综合目录。
Genome Biol. 2019 Jan 3;20(1):1. doi: 10.1186/s13059-018-1612-0.
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MaxMIF: A New Method for Identifying Cancer Driver Genes through Effective Data Integration.MaxMIF：一种通过有效数据整合识别癌症驱动基因的新方法。
Adv Sci (Weinh). 2018 Jul 23;5(9):1800640. doi: 10.1002/advs.201800640. eCollection 2018 Sep.
9
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AFF4 promotes tumorigenesis and tumor-initiation capacity of head and neck squamous cell carcinoma cells by regulating SOX2.AFF4 通过调控 SOX2 促进头颈部鳞状细胞癌细胞的致瘤性和肿瘤起始能力。
Carcinogenesis. 2018 Jul 3;39(7):937-947. doi: 10.1093/carcin/bgy046.