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PLoS One January 1, 2015; 10 (7): e0131832.

Predicting Variabilities in Cardiac Gene Expression with a Boolean Network Incorporating Uncertainty.

Grieb M , Burkovski A , Sträng JE , Kraus JM , Groß A , Palm G , Kühl M , Kestler HA .

Gene interactions in cells can be represented by gene regulatory networks. A Boolean network models gene interactions according to rules where gene expression is represented by binary values (on / off or {1, 0}). In reality, however, the gene''s state can have multiple values due to biological properties. Furthermore, the noisy nature of the experimental design results in uncertainty about a state of the gene. Here we present a new Boolean network paradigm to allow intermediate values on the interval [0, 1]. As in the Boolean network, fixed points or attractors of such a model correspond to biological phenotypes or states. We use our new extension of the Boolean network paradigm to model gene expression in first and second heart field lineages which are cardiac progenitor cell populations involved in early vertebrate heart development. By this we are able to predict additional biological phenotypes that the Boolean model alone is not able to identify without utilizing additional biological knowledge. The additional phenotypes predicted by the model were confirmed by published biological experiments. Furthermore, the new method predicts gene expression propensities for modelled but yet to be analyzed genes.

PubMed ID: 26207376
PMC ID: PMC4514755
Article link: PLoS One

Species referenced: Xenopus
Genes referenced: alcam aplnr bmp2 bmp4 cdh2 dkk1 fgf8 foxc1 foxh1 fuz gata6 isl1 kdr mef2d nkx2-5 ror2 shf tbx1 tbx20 tbx5 tnni3

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References [+] :
Abu-Issa, Heart field: from mesoderm to heart tube. 2007, Pubmed