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000177188 041__ $$aEnglish
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000177188 1001_ $$0P:(DE-HGF)0$$aTares, Kira$$b0$$eFirst author
000177188 245__ $$aThe canonical and non-canonical NF-κB pathways and their crosstalk: A comparative study based on Petri nets.
000177188 260__ $$aAmsterdam [u.a.]$$bElsevier Science$$c2022
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000177188 500__ $$a#EA:C070# / 2022 Jan;211:104564
000177188 520__ $$aNF-κB is a protein complex that occurs in almost all animal cell types. It regulates the cellular immune responses to stimuli in the nucleus. Dysregulation of NF-κB can cause severe diseases like chronic inflammation, autoimmune diseases or cancer. We modeled the two major pathways leading from the external cellular stimulation of the CD40 receptor to the nuclear translocation of NF-κB dimers, the canonical and non-canonical pathway. Based on literature data, we developed two Petri net models describing these pathways. In a third Petri net, we combined the two models, introducing crosstalk specific in CD40L-stimulated B cells. In terms of structural properties, we checked the Petri nets for their consistency and correctness. To explore differences and similarities, we compared structural properties and the simulation behavior of the models. The non-canonical NF-κB pathway exhibited a more diverse regulation than the canonical pathway. Applying in silico knockout analyses, we were able to quantify the relevance of individual biochemical processes. We predicted interrelationships, e.g., between the synthesis of the protein NF-κB-inducing kinase and the processing of the precursor protein p100. The activation of the transcription factors, p50-RelA and p52-RelB, was affected by most of the knockouts. The results of the in silico knockout were in accordance with experimental studies. The Petri net models provide a basis for further analyses and could be extended to include gene expression, additional pathways, molecular processes, and kinetic data.
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000177188 650_7 $$2Other$$aCanonical
000177188 650_7 $$2Other$$aInsilico knockout matrix
000177188 650_7 $$2Other$$aInvariants
000177188 650_7 $$2Other$$aManatee invariants
000177188 650_7 $$2Other$$aNF-kB pathway
000177188 650_7 $$2Other$$aNon-canonical
000177188 650_7 $$2Other$$aPetri nets
000177188 7001_ $$aAckermann, J Org$$b1
000177188 7001_ $$aKoch, Ina$$b2
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