The Network Zoo: a multilingual package for the inference and analysis of biological networks
The Network Zoo: a multilingual package for the inference and analysis of biological networks
Abstract Inference and analysis of cellular biological networks requires software tools that integrate multi-omic data from various sources. The Network Zoo (netZoo; netzoo.github.io) is an open-source software suite to model biological networks, including context-specific gene regulatory networks and multi-omics partial correlation networks, to conduct differential analyses, estimate community structure, and model the transitions between biological states. The netZoo builds on our ongoing development of network methods, harmonizing the implementations in various computing languages (R, Python, MATLAB, and C) and between methods to allow a better integration of these tools into analytical pipelines. To demonstrate the value of this integrated toolkit, we analyzed the multi-omic data from the Cancer Cell Line Encyclopedia (CCLE) by inferring gene regulatory networks for each cancer cell line and associating network features with other phenotypic attributes such as drug sensitivity. This allowed us to identify transcription factors that play a critical role in both drug resistance and cancer development in melanoma. We also used netZoo to build a pan-cancer, multi-tiered CCLE map and used it to identify known metabolic hallmarks of cancer and to estimate novel context-specific elements that mediate post-transcriptional regulation. Because the netZoo tools are open-source and there is a growing community of both users and developers, we built an ecosystem to support community contributions, share use cases, and visualize networks online. As additional data types become available and our suite of methods grows, we will expand “the zoo” to incorporate an increasingly sophisticated collection of tools for network inference and analysis.
Wang Tian、Weighill Deborah、Schlauch Daniel、Paulson Joseph N.、Altenbuchinger Michael、van Ijzendoorn David、Song Alex、DeMeo Dawn、Padi Megha、Platig John、Morgan Daniel、Calderer Genis、Lim James、Lopes-Ramos Camila M.、Kuijjer Marieke L.、Fanfani Viola、Chen Cho-Yi、Burkholz Rebekka、Quackenbush John、Guebila Marouen Ben、Shutta Kate、Sonanwane Abhijeet、Marin Alessandro、Glass Kimberly
Department of Biostatistics, Harvard T.H. Chan School of Public Health||Biology Department, Boston CollegeDepartment of Biostatistics, Harvard T.H. Chan School of Public Health||Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel HillDepartment of Biostatistics, Harvard T.H. Chan School of Public Health||Genospace, LLCDepartment of Biochemistry and Molecular Biology, Pennsylvania State University College of MedicineDepartment of Biostatistics, Harvard T.H. Chan School of Public Health||Department of Medical Bioinformatics, University Medical Center G?ttingenDepartment of Pathology, Leiden University Medical Center||Department of Pathology, Stanford University School of MedicineChanning Division of Network Medicine, Brigham and Women?ˉs Hospital||Computational Biology Department, Carnegie Mellon UniversityChanning Division of Network Medicine, Brigham and Women?ˉs HospitalDepartment of Molecular and Cellular Biology, University of ArizonaChanning Division of Network Medicine, Brigham and Women?ˉs HospitalChanning Division of Network Medicine, Brigham and Women?ˉs Hospital||Hong Kong University, School of Biomedical SciencesCenter for Molecular Medicine Norway, Nordic EMBL Partnership, University of OsloDepartment of Molecular and Cellular Biology, University of Arizona||Monoceros Biosystems, LLCDepartment of Biostatistics, Harvard T.H. Chan School of Public Health||Channing Division of Network Medicine, Brigham and Women?ˉs HospitalCenter for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo||Department of Pathology, Leiden University Medical Center||Leiden Center for Computational Oncology, Leiden UniversityDepartment of Biostatistics, Harvard T.H. Chan School of Public HealthDepartment of Biostatistics, Harvard T.H. Chan School of Public Health||Dana-Farber Cancer Institute||Institute of Biomedical Informatics, National Yang Ming Chiao Tung UniversityDepartment of Biostatistics, Harvard T.H. Chan School of Public Health||CISPA Helmholtz Center for Information SecurityDepartment of Biostatistics, Harvard T.H. Chan School of Public Health||Channing Division of Network Medicine, Brigham and Women?ˉs Hospital||Dana-Farber Cancer InstituteDepartment of Biostatistics, Harvard T.H. Chan School of Public HealthDepartment of Biostatistics, Harvard T.H. Chan School of Public Health||Channing Division of Network Medicine, Brigham and Women?ˉs HospitalChanning Division of Network Medicine, Brigham and Women?ˉs Hospital||Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women?ˉs HospitalExpert Analytics ASDepartment of Biostatistics, Harvard T.H. Chan School of Public Health||Channing Division of Network Medicine, Brigham and Women?ˉs Hospital
生物科学研究方法、生物科学研究技术计算技术、计算机技术分子生物学
gene regulationmulti-omic modelingnetwork biologyopen-source software
Wang Tian,Weighill Deborah,Schlauch Daniel,Paulson Joseph N.,Altenbuchinger Michael,van Ijzendoorn David,Song Alex,DeMeo Dawn,Padi Megha,Platig John,Morgan Daniel,Calderer Genis,Lim James,Lopes-Ramos Camila M.,Kuijjer Marieke L.,Fanfani Viola,Chen Cho-Yi,Burkholz Rebekka,Quackenbush John,Guebila Marouen Ben,Shutta Kate,Sonanwane Abhijeet,Marin Alessandro,Glass Kimberly.The Network Zoo: a multilingual package for the inference and analysis of biological networks[EB/OL].(2025-03-28)[2025-06-13].https://www.biorxiv.org/content/10.1101/2022.05.30.494077.点此复制
评论