Statistical ensemble of gene regulatory networks of macrophage differentiation

BMC Bioinformatics

Research

Alessandro Palma¹  Abdul Salam Jarrah²  Paolo Tieri³  Filippo Castiglione³ 

[1] Department of Biology, University of Tor Vergata, Via della ricerca scientifica 1, 00133, Rome, Italy;Department of Mathematics and Statistics, American University of Sharjah, P.O.Box 26666, Sharjah, UAE;Institute for Applied Computing, National Research Council of Italy, Via dei Taurini 19, 00185, Rome, Italy;

关键词: Macrophage differentiation;    Gene regulatory network;    Agent-based modelling;    Multiscale modelling;   

DOI  :  10.1186/s12859-016-1363-4

来源: Springer

【 摘 要 】

BackgroundMacrophages cover a major role in the immune system, being the most plastic cell yielding several key immune functions.MethodsHere we derived a minimalistic gene regulatory network model for the differentiation of macrophages into the two phenotypes M1 (pro-) and M2 (anti-inflammatory).ResultsTo test the model, we simulated a large number of such networks as in a statistical ensemble. In other words, to enable the inter-cellular crosstalk required to obtain an immune activation in which the macrophage plays its role, the simulated networks are not taken in isolation but combined with other cellular agents, thus setting up a discrete minimalistic model of the immune system at the microscopic/intracellular (i.e., genetic regulation) and mesoscopic/intercellular scale.ConclusionsWe show that within the mesoscopic level description of cellular interaction and cooperation, the gene regulatory logic is coherent and contributes to the overall dynamics of the ensembles that shows, statistically, the expected behaviour.

【 授权许可】

CC BY   
© The Author(s) 2016

【 图 表 】

Fig. 18

12888_2023_5206_Article_IEq3.gif

Fig. 17

12888_2023_5206_Article_IEq1.gif

Fig. 16

Fig. 1

Fig. 15

Fig. 3

Fig. 14

Fig. 2