Literature DB >> 20023717

The powerful law of the power law and other myths in network biology.

Gipsi Lima-Mendez1, Jacques van Helden.   

Abstract

For almost 10 years, topological analysis of different large-scale biological networks (metabolic reactions, protein interactions, transcriptional regulation) has been highlighting some recurrent properties: power law distribution of degree, scale-freeness, small world, which have been proposed to confer functional advantages such as robustness to environmental changes and tolerance to random mutations. Stochastic generative models inspired different scenarios to explain the growth of interaction networks during evolution. The power law and the associated properties appeared so ubiquitous in complex networks that they were qualified as "universal laws". However, these properties are no longer observed when the data are subjected to statistical tests: in most cases, the data do not fit the expected theoretical models, and the cases of good fitting merely result from sampling artefacts or improper data representation. The field of network biology seems to be founded on a series of myths, i.e. widely believed but false ideas. The weaknesses of these foundations should however not be considered as a failure for the entire domain. Network analysis provides a powerful frame for understanding the function and evolution of biological processes, provided it is brought to an appropriate level of description, by focussing on smaller functional modules and establishing the link between their topological properties and their dynamical behaviour.

Mesh:

Year:  2009        PMID: 20023717     DOI: 10.1039/b908681a

Source DB:  PubMed          Journal:  Mol Biosyst        ISSN: 1742-2051


  52 in total

1.  Topological analysis and interactive visualization of biological networks and protein structures.

Authors:  Nadezhda T Doncheva; Yassen Assenov; Francisco S Domingues; Mario Albrecht
Journal:  Nat Protoc       Date:  2012-03-15       Impact factor: 13.491

Review 2.  Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system.

Authors:  Bram Stynen; Hélène Tournu; Jan Tavernier; Patrick Van Dijck
Journal:  Microbiol Mol Biol Rev       Date:  2012-06       Impact factor: 11.056

3.  An exponential random graph modeling approach to creating group-based representative whole-brain connectivity networks.

Authors:  Sean L Simpson; Malaak N Moussa; Paul J Laurienti
Journal:  Neuroimage       Date:  2012-01-17       Impact factor: 6.556

Review 4.  Architecture, constraints, and behavior.

Authors:  John C Doyle; Marie Csete
Journal:  Proc Natl Acad Sci U S A       Date:  2011-07-25       Impact factor: 11.205

5.  Cluster Analysis of Medicinal Plants and Targets Based on Multipartite Network.

Authors:  Namgil Lee; Hojin Yoo; Heejung Yang
Journal:  Biomolecules       Date:  2021-04-08

6.  Identification of reaction organization patterns that naturally cluster enzymatic transformations.

Authors:  Carlos Vazquez-Hernandez; Antonio Loza; Esteban Peguero-Sanchez; Lorenzo Segovia; Rosa-Maria Gutierrez-Rios
Journal:  BMC Syst Biol       Date:  2018-05-30

Review 7.  Microbial interactions: from networks to models.

Authors:  Karoline Faust; Jeroen Raes
Journal:  Nat Rev Microbiol       Date:  2012-07-16       Impact factor: 60.633

8.  Small protein folds at the root of an ancient metabolic network.

Authors:  Hagai Raanan; Saroj Poudel; Douglas H Pike; Vikas Nanda; Paul G Falkowski
Journal:  Proc Natl Acad Sci U S A       Date:  2020-03-18       Impact factor: 11.205

9.  Novel insights through the integration of structural and functional genomics data with protein networks.

Authors:  Declan Clarke; Nitin Bhardwaj; Mark B Gerstein
Journal:  J Struct Biol       Date:  2012-02-11       Impact factor: 2.867

10.  Data-driven insights into deletions of Mycobacterium tuberculosis complex chromosomal DR region using spoligoforests.

Authors:  Cagri Ozcaglar; Amina Shabbeer; Natalia Kurepina; Bülent Yener; Kristin P Bennett
Journal:  Proceedings (IEEE Int Conf Bioinformatics Biomed)       Date:  2011
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