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The structure balance of gene-gene networks beyond pairwise interactions

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  • Nastaran Allahyari
  • Amir Kargaran
  • Ali Hosseiny
  • G R Jafari

Abstract

Despite its high and direct impact on nearly all biological processes, the underlying structure of gene-gene interaction networks is investigated so far according to pair connections. To address this, we explore the gene interaction networks of the yeast Saccharomyces cerevisiae beyond pairwise interaction using the structural balance theory (SBT). Specifically, we ask whether essential and nonessential gene interaction networks are structurally balanced. We study triadic interactions in the weighted signed undirected gene networks and observe that balanced and unbalanced triads are over and underrepresented in both networks, thus beautifully in line with the strong notion of balance. Moreover, we note that the energy distribution of triads is significantly different in both essential and nonessential networks compared to the shuffled networks. Yet, this difference is greater in the essential network regarding the frequency as well as the energy of triads. Additionally, results demonstrate that triads in the essential gene network are more interconnected through sharing common links, while in the nonessential network they tend to be isolated. Last but not least, we investigate the contribution of all-length signed walks and its impact on the degree of balance. Our findings reveal that interestingly when considering longer cycles, not only, both essential and nonessential gene networks are more balanced compared to their corresponding shuffled networks, but also, the nonessential gene network is more balanced compared to the essential network.

Suggested Citation

  • Nastaran Allahyari & Amir Kargaran & Ali Hosseiny & G R Jafari, 2022. "The structure balance of gene-gene networks beyond pairwise interactions," PLOS ONE, Public Library of Science, vol. 17(3), pages 1-18, March.
  • Handle: RePEc:plo:pone00:0258596
    DOI: 10.1371/journal.pone.0258596
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    1. repec:cup:cbooks:9780511771576 is not listed on IDEAS
    2. XueZhong Zhou & Jörg Menche & Albert-László Barabási & Amitabh Sharma, 2014. "Human symptoms–disease network," Nature Communications, Nature, vol. 5(1), pages 1-10, September.
    3. Easley,David & Kleinberg,Jon, 2010. "Networks, Crowds, and Markets," Cambridge Books, Cambridge University Press, number 9780521195331, September.
    4. Andres M Belaza & Kevin Hoefman & Jan Ryckebusch & Aaron Bramson & Milan van den Heuvel & Koen Schoors, 2017. "Statistical physics of balance theory," PLOS ONE, Public Library of Science, vol. 12(8), pages 1-19, August.
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