Pathway-resolved decomposition demonstrates correlation and noise dependencies of redundant information processing in recurrent feed-forward topologies

Biswas, Ayan

doi:10.1103/physreve.105.034406

Cited by 2 publications

(6 citation statements)

References 57 publications

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“…Mangan and Alon [6] studied the deterministic dynamics of FFLs. Fluctuation propagation and its relation to the architecture of CFFLs have been studied earlier [18][19][20][21][22]. CFFLs were found to have efficient fluctuation propagation properties along the cascade [23].…”

Section: Introductionmentioning

confidence: 99%

“…Theoretic analysis reveals C1-FFL as an efficient information transmission motif [21]. A pathway-based decomposition of the output fluctuations addressed the redundant information processing capacity of C1-and I1-FFL [22].…”

Section: Introductionmentioning

confidence: 99%

“…Since one of the two inputs coming from parallel (direct and indirect) pathways is enough to regulate the target gene expression in the additive integration mechanism, a competition between the inputs is in action and depends on the necessary binding constant K. In the multiplicative integration mechanism, however, such competition disappears as both inputs are necessary for target gene regulation. Theoretical analysis reveals an additional fluctuation term that appears due to the integration of OSC and TSC [21,22,25]. The additional fluctuations (or cross-interaction) originate due to the lateral overlap of the two parallel pathways (direct and indirect) as shown in figure 1.…”

Section: Introductionmentioning

confidence: 99%

“…In the present manuscript, we quantify the output fluctuations by measuring the coefficient of variation (CV) of output Y. To understand the nature of fluctuation propagation in CFFLs, we opt for the strategy of fluctuation decomposition reported earlier [21,22,25,27,28]. Fluctuation decomposition has been developed to quantify the gene expression mechanism in noisy environments [27].…”

Section: Introductionmentioning

confidence: 99%

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Interplay of degeneracy and non-degeneracy in fluctuation propagation in coherent feed-forward loop motif

Subhra Roy,

Nandi,

Chaudhury

et al. 2023

J. Stat. Mech.

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We present a stochastic framework to decipher fluctuation propagation in classes of coherent feed-forward loops (CFFLs). The systematic contribution of the direct (one-step) and indirect (two-step) pathways is considered to quantify fluctuations of the output node. We also consider both additive and multiplicative integration mechanisms of the two parallel pathways (one-step and two-step). Analytical expression of the output node’s coefficient of variation shows contributions of intrinsic, one-step, two-step, and cross-interaction in closed form. We observe a diverse range of degeneracy and non-degeneracy in each of the decomposed fluctuation terms and their contribution to the overall output fluctuations of each CFFL motif. The analysis of output fluctuations reveals a maximal level of fluctuations of the CFFL motif of type 1.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Interplay of degeneracy and non-degeneracy in fluctuation propagation in coherent feed-forward loop motif

Subhra Roy,

Nandi,

Chaudhury

et al. 2023

J. Stat. Mech.

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“…Others have opined in favor of minimized output noise as a plausible feature, promoting the recurrence of C1-FFL within the family of coherent FFLs [5,6]. Since information is nontrivially intertwined with noise [7][8][9], we take a fresh approach here to investigate the effects of genetic regulation on information transmission in the C1-FFL motif. In this connection, we mention that the imprint of network topology invariably appears on the biochemical noise transduction [10,11].…”

Section: Introductionmentioning

confidence: 99%

The role of gene regulation in redundant and synergistic information transfers in coherent feed-forward loop

Momin¹,

Biswas²

2023

J. Stat. Mech.

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For the ubiquitous coherent type-1 feed-forward loop (C1-FFL) motif, the master and co-regulators act as sources of information in decoding the output gene expression state. Using the variance-based definition of information within a Gaussian framework at steady state, we apply the partial information decomposition technique to quantify the redundant (common) and synergistic (complementary) information transfers to the output gene. By enabling the generic C1-FFL motif with complementarily tunable regulatory pathways and fixed gene product abundances, we examine the role of output gene regulation in maintaining the flow of these two multivariate information flavors. We find that the redundant and synergistic information transfers are simultaneously maximized when the direct and indirect output regulatory strengths are nearly balanced. All other manifestations of the generic C1-FFL motif, including the two terminal ones, namely, the two-step cascade and fan-out, transduce lesser amounts of these two types of information. This optimal decoding of the output gene expression state by a nearly balanced C1-FFL motif holds true in an extended repertoire of biologically relevant parametric situations. These realizations involve additional layers of regulation through changing gene product abundances, activation coefficients, and degradation rates. Our analyses underline the regulatory mechanisms through which the C1-FFL motif is able to optimally reduce its output uncertainty concurrently via redundant and synergistic modes of information transfer. We find that these information transfers are guided by fluctuations in the motif. The prevalence of redundancy over synergy in all regulatory implementations is also noteworthy.

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Pathway-resolved decomposition demonstrates correlation and noise dependencies of redundant information processing in recurrent feed-forward topologies

Cited by 2 publications

References 57 publications

Interplay of degeneracy and non-degeneracy in fluctuation propagation in coherent feed-forward loop motif

Interplay of degeneracy and non-degeneracy in fluctuation propagation in coherent feed-forward loop motif

The role of gene regulation in redundant and synergistic information transfers in coherent feed-forward loop

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