NetBID2 provides comprehensive hidden driver analysis.
NetBID2 provides comprehensive hidden driver analysis.
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DOI：
10.1038/s41467-023-38335-6
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发表时间：
2023-05-04
影响因子：
16.6
通讯作者：
Yu, Jiyang
中科院分区：
文献类型：
--
作者：
Dong, Xinran;Ding, Liang;Thrasher, Andrew;Wang, Xinge;Liu, Jingjing;Pan, Qingfei;Rash, Jordan;Dhungana, Yogesh;Yang, Xu;Risch, Isabel;Li, Yuxin;Yan, Lei;Rusch, Michael;McLeod, Clay;Yan, Koon-Kiu;Peng, Junmin;Chi, Hongbo;Zhang, Jinghui;Yu, Jiyang
许多被称为“隐藏”驱动因素的信号传导和其他基因可能不会在 mRNA 或蛋白质水平上发生遗传或表观遗传改变或差异表达，而是通过翻译后修饰或其他机制驱动表型，例如肿瘤发生。然而，基于基因组学或差异表达的传统方法在暴露此类隐藏驱动因素方面受到限制。在这里，我们提出了一个全面的算法和工具包 NetBID2（数据驱动的基于网络的驱动程序贝叶斯推理，版本 2），它对上下文特定的交互组进行逆向工程，并集成从大规模多组学数据推断的网络活动，从而能够识别传统分析无法检测到的隐藏驱动程序。 NetBID2通过提供多功能数据可视化和复杂的统计分析，对之前的原型版本进行了大幅重新设计，这极大地方便了研究人员通过端到端多组学数据分析来解释结果。我们使用三个隐藏驱动程序示例来演示 NetBID2 的强大功能。我们在正常组织以及儿科和成人癌症中部署了具有 145 个特定背景基因调控和信号网络的 NetBID2 Viewer、Runner 和云应用程序，以促进端到端分析、实时交互式可视化和基于云的数据共享。 NetBID2 可在 https://jyyulab.github.io/NetBID 免费获取。捕获可能没有基因改变或没有从组学数据中差异表达的“隐藏”驱动因素是一项挑战。在此，作者开发了 NetBID2，这是一个基于网络的综合工具箱，具有多种功能，能够集成多组学数据以暴露此类隐藏的驱动程序。
Many signaling and other genes known as “hidden” drivers may not be genetically or epigenetically altered or differentially expressed at the mRNA or protein levels, but, rather, drive a phenotype such as tumorigenesis via post-translational modification or other mechanisms. However, conventional approaches based on genomics or differential expression are limited in exposing such hidden drivers. Here, we present a comprehensive algorithm and toolkit NetBID2 (data-driven network-based Bayesian inference of drivers, version 2), which reverse-engineers context-specific interactomes and integrates network activity inferred from large-scale multi-omics data, empowering the identification of hidden drivers that could not be detected by traditional analyses. NetBID2 has substantially re-engineered the previous prototype version by providing versatile data visualization and sophisticated statistical analyses, which strongly facilitate researchers for result interpretation through end-to-end multi-omics data analysis. We demonstrate the power of NetBID2 using three hidden driver examples. We deploy NetBID2 Viewer, Runner, and Cloud apps with 145 context-specific gene regulatory and signaling networks across normal tissues and paediatric and adult cancers to facilitate end-to-end analysis, real-time interactive visualization and cloud-based data sharing. NetBID2 is freely available at https://jyyulab.github.io/NetBID. It’s challenging to capture “hidden” drivers that may not be genetically-altered or differentially-expressed from omics data. Here the authors developed NetBID2, a comprehensive network-based toolbox with versatile features, enabling the integration of multi-omics data to expose such hidden drivers.
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DOI：
10.1038/nrc.2016.124
发表时间：
2017-03
期刊：
Nature reviews. Cancer
影响因子：
--
作者：
Califano A;Alvarez MJ
通讯作者：
Alvarez MJ
影响因子：
30.8
作者：
Liu Y;Easton J;Shao Y;Maciaszek J;Wang Z;Wilkinson MR;McCastlain K;Edmonson M;Pounds SB;Shi L;Zhou X;Ma X;Sioson E;Li Y;Rusch M;Gupta P;Pei D;Cheng C;Smith MA;Auvil JG;Gerhard DS;Relling MV;Winick NJ;Carroll AJ;Heerema NA;Raetz E;Devidas M;Willman CL;Harvey RC;Carroll WL;Dunsmore KP;Winter SS;Wood BL;Sorrentino BP;Downing JR;Loh ML;Hunger SP;Zhang J;Mullighan CG
通讯作者：
Mullighan CG
影响因子：
28.2
作者：
Mundi, Prabhjot S.;Cruz, Filemon S. Dela;Grunn, Adina;Diolaiti, Daniel;Mauguen, Audrey;Rainey, Allison R.;Guillan, Kristina;Siddiquee, Armaan;You, Daoqi;Realubit, Ronald;Karan, Charles;Ortiz, Michael V.;Douglass, Eugene F.;Accordino, Melissa;Mistretta, Suzanne;Brogan, Frances;Bruce, Jeffrey N.;Caescu, Cristina I.;Carvajal, Richard D.;Crew, Katherine D.;Decastro, Guarionex;Heaney, Mark;Henick, Brian S.;Hershman, Dawn L.;Hou, June Y.;Iwamoto, Fabio M.;Jurcic, Joseph G.;Kiran, Ravi P.;Kluger, Michael D.;Kreisl, Teri;Lamanna, Nicole;Lassman, Andrew B.;Lim, Emerson A.;Manji, Gulam A.;Mckhann, Guy M.;Mckiernan, James M.;Neugut, Alfred I.;Olive, Kenneth P.;Rosenblat, Todd;Schwartz, Gary K.;Shu, Catherine A.;Sisti, Michael B.;Tergas, Ana;Vattakalam, Reena M.;Welch, Mary;Wenske, Sven;Wright, Jason D.;Canoll, Peter;Hibshoosh, Hanina;Kalinsky, Kevin;Aburi, Mahalaxmi;Sims, Peter A.;Alvarez, Mariano J.;Kung, Andrew L.;Califano, Andrea
通讯作者：
Califano, Andrea
影响因子：
56.9
作者：
Kim, Minkyu;Park, Jisoo;Bouhaddou, Mehdi;Kim, Kyumin;Rojc, Ajda;Modak, Maya;Soucheray, Margaret;McGregor, Michael J.;O'Leary, Patrick;Wolf, Denise;Stevenson, Erica;Foo, Tzeh Keong;Mitchell, Dominique;Herrington, Kari A.;Munoz, Denise P.;Tutuncuoglu, Beril;Chen, Kuei-Ho;Zheng, Fan;Kreisberg, Jason F.;Diolaiti, Morgan E.;Gordan, John D.;Coppe, Jean-Philippe;Swaney, Danielle L.;Xia, Bing;van 't Veer, Laura;Ashworth, Alan;Ideker, Trey;Krogan, Nevan J.
通讯作者：
Krogan, Nevan J.
影响因子：
16.2
作者：
Bai, Bing;Wang, Xusheng;Peng, Junmin
通讯作者：
Peng, Junmin