2020
DOI: 10.1186/s12859-020-03778-x
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Signaling pathways have an inherent need for noise to acquire information

Abstract: Background All living systems acquire information about their environment. At the cellular level, they do so through signaling pathways. Such pathways rely on reversible binding interactions between molecules that detect and transmit the presence of an extracellular cue or signal to the cell’s interior. These interactions are inherently stochastic and thus noisy. On the one hand, noise can cause a signaling pathway to produce the same response for different stimuli, which reduces the amount of … Show more

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Cited by 13 publications
(8 citation statements)
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References 89 publications
(126 reference statements)
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“…1 ( Kanehisa et al, 2017 ). Modeling a small-sized network is a challenging task because a small number of molecular interactions limit the overall dynamic range of the signals ( Tkačik et al, 2009 ; Azpeitia et al, 2020 ). Therefore, we discarded KEGG pathways having less than 30 edges from the interactome evaluations.…”
Section: Methodsmentioning
confidence: 99%
“…1 ( Kanehisa et al, 2017 ). Modeling a small-sized network is a challenging task because a small number of molecular interactions limit the overall dynamic range of the signals ( Tkačik et al, 2009 ; Azpeitia et al, 2020 ). Therefore, we discarded KEGG pathways having less than 30 edges from the interactome evaluations.…”
Section: Methodsmentioning
confidence: 99%
“…For the above CSTR-based systems, typical response times to changing input are on the order of seconds, [64] which compares to response times for post-translational modifications. Typical half-lives of signaling molecules within biological systems, to further compare, such as for example, nitrous oxide, [12,69] mRNA, and proteins [70,71] are a few seconds, seconds to hours, and hours to days, respectively. Lastly, messengers like norepinephrine and dopamine, have half-lives between 10 s and 100 s. [12] These values are quite comparable to fluctuations in CSTRs.…”
Section: Molecular Decision-making For Communicationmentioning
confidence: 99%
“…Each pathway within a biomolecular network requires input cues from the extracellular environment for onward downstream signal transduction (133)(134)(135). In the case of cancer, the biomolecular milieu constituting the tumor microenvironment (TME) acts as a niche for tumor development, metastasis, as well as therapy response (136) (Figure 1E and Table S4).…”
Section: Cellular Environment Databasesmentioning
confidence: 99%