Theoretical knock-outs on biological networks

Pedro J Miranda (Corresponding Author), Sandro E de S Pinto, Murilo S Baptista, Giuliano G La Guardia

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Abstract

In this work we formalize a method to compute the degree of importance of biological agents that participates on the dynamics of a biological phenomenon build upon a complex network. We call this new procedure by theoretical knock-out (KO). To devise this method, we make two approaches: algebraically and algorithmically. In both cases we compute a vector on an asymptotic state, called flux vector. The flux is given by a random walk on a directed graph that represents a biological phenomenon. This vector gives us the information about the relative flux of walkers on a vertex which represents a biological agent. With two vector of this kind, we can calculate the relative mean error between them by averaging over its coefficients. This quantity allows us to assess the degree of importance of each vertex of a complex network that evolves in time and has experimental background. We find out that this procedure can be applied in any sort of biological phenomena in which we can know the role and interrelationships of its agents. These results also provide experimental biologists to predict the order of importance of biological agents on a mounted complex network.
Original languageEnglish
Pages (from-to)38-44
Number of pages9
JournalJournal of Theoretical Biology
Volume403
Early online date14 May 2016
DOIs
Publication statusPublished - 21 Aug 2016

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Biological Networks
Biological Phenomena
Complex networks
Biological Factors
Complex Networks
Fluxes
biologists
Walkers
Directed graphs
Vertex of a graph
methodology
Directed Graph
Sort
Averaging
Random walk
Calculate
Predict
Coefficient

Keywords

  • q-bio.MN
  • relational biology
  • (M, R)-system
  • complex networks
  • random walks
  • theoretical KOs

Cite this

Theoretical knock-outs on biological networks. / Miranda, Pedro J (Corresponding Author); Pinto, Sandro E de S; Baptista, Murilo S; La Guardia, Giuliano G.

In: Journal of Theoretical Biology, Vol. 403, 21.08.2016, p. 38-44.

Research output: Contribution to journalArticle

Miranda, Pedro J ; Pinto, Sandro E de S ; Baptista, Murilo S ; La Guardia, Giuliano G. / Theoretical knock-outs on biological networks. In: Journal of Theoretical Biology. 2016 ; Vol. 403. pp. 38-44.
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