The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks

Marouen Ben Guebila; Tian Wang; Camila M Lopes-Ramos; Viola Fanfani; Des Weighill; Rebekka Burkholz; Daniel Schlauch; Joseph N Paulson; Michael Altenbuchinger; Katherine H Shutta; Abhijeet R Sonawane; James Lim; Genis Calderer; David G P van IJzendoorn; Daniel Morgan; Alessandro Marin; Cho-Yi Chen; Qi Song; Enakshi Saha; Dawn L DeMeo; Megha Padi; John Platig; Marieke L Kuijjer; Kimberly Glass; John Quackenbush

doi:10.1186/s13059-023-02877-1

The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks

Genome Biol. 2023 Mar 9;24(1):45. doi: 10.1186/s13059-023-02877-1.

Authors

Marouen Ben Guebila¹, Tian Wang^{1

2}, Camila M Lopes-Ramos^{1

3}, Viola Fanfani¹, Des Weighill^{1

4}, Rebekka Burkholz^{1

5}, Daniel Schlauch^{1

6}, Joseph N Paulson⁷, Michael Altenbuchinger^{1

8}, Katherine H Shutta^{1

3}, Abhijeet R Sonawane^{3

9}, James Lim^{10

11}, Genis Calderer¹², David G P van IJzendoorn^{13

14}, Daniel Morgan^{3

15}, Alessandro Marin¹⁶, Cho-Yi Chen^{1

17

18}, Qi Song^{3

19}, Enakshi Saha¹, Dawn L DeMeo³, Megha Padi¹⁰, John Platig³, Marieke L Kuijjer^{12

13

20}, Kimberly Glass^{1

3}, John Quackenbush^{21

22

23}

Affiliations

¹ Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
² Present Address: Biology Department, Boston College, Chestnut Hill, MA, USA.
³ Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
⁴ Present Address: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
⁵ Present Address: CISPA Helmholtz Center for Information Security, Saarbrücken, Germany.
⁶ Present Address: Genospace, LLC, Boston, MA, USA.
⁷ Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
⁸ Present Address: Department of Medical Bioinformatics, University Medical Center Göttingen, Göttingen, Germany.
⁹ Present Address: Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
¹⁰ Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA.
¹¹ Present Address: Monoceros Biosystems, LLC, San Diego, CA, USA.
¹² Center for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo, Oslo, Norway.
¹³ Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
¹⁴ Present Address: Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA.
¹⁵ Present Address: School of Biomedical Sciences, Hong Kong University, Pokfulam, Hong Kong.
¹⁶ Expert Analytics AS, Oslo, Norway.
¹⁷ Dana-Farber Cancer Institute, Boston, MA, USA.
¹⁸ Present Address: Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan.
¹⁹ Present Address: Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
²⁰ Leiden Center for Computational Oncology, Leiden University, Leiden, The Netherlands.
²¹ Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA. johnq@hsph.harvard.edu.
²² Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. johnq@hsph.harvard.edu.
²³ Dana-Farber Cancer Institute, Boston, MA, USA. johnq@hsph.harvard.edu.

Abstract

Inference and analysis of gene regulatory networks (GRNs) require software that integrates multi-omic data from various sources. The Network Zoo (netZoo; netzoo.github.io) is a collection of open-source methods to infer GRNs, conduct differential network analyses, estimate community structure, and explore the transitions between biological states. The netZoo builds on our ongoing development of network methods, harmonizing the implementations in various computing languages and between methods to allow better integration of these tools into analytical pipelines. We demonstrate the utility using multi-omic data from the Cancer Cell Line Encyclopedia. We will continue to expand the netZoo to incorporate additional methods.

Keywords: Gene regulation; Multi-omic analysis; Network biology; Open-source software.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

Algorithms
Computational Biology / methods
Gene Regulatory Networks*
Humans
Multiomics
Neoplasms*
Software

Abstract

Publication types

MeSH terms

Grants and funding