scholarly journals Incoherent feedforward motifs as immune change detectors

2015 ◽  
Author(s):  
Eduardo Sontag
Keyword(s):  
Change Detection ◽  
Scale Invariance ◽  
Fold Change ◽  
Fold Change Detection

We speculate that incoherent feedforward loops may be phenomenologically involved in self/nonself discrimination in immune-infection and immune-tumor interactions, acting as "change detectors". In turn, this may result in logarithmic sensing (Weber phenomenon) and even scale invariance (fold-change detection).

scholarly journals An empirical bayesian approach for testing gene expression fold change and its application in detecting global dosage effects

2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Zhenxing Guo ◽  
Ying Cui ◽  
Xiaowen Shi ◽  
James A Birchler ◽  
Igor Albizua ◽  
...  
Keyword(s):  
Gene Expression ◽  
Change Detection ◽  
Bayesian Approach ◽  
Variance Estimation ◽  
T Test ◽  
Fold Change ◽  
Empirical Bayesian ◽  
Biological Studies ◽  
Fold Change Detection ◽  
Empirical Bayesian Approach

Abstract We are motivated by biological studies intended to understand global gene expression fold change. Biologists have generally adopted a fixed cutoff to determine the significance of fold changes in gene expression studies (e.g. by using an observed fold change equal to two as a fixed threshold). Scientists can also use a t-test or a modified differential expression test to assess the significance of fold changes. However, these methods either fail to take advantage of the high dimensionality of gene expression data or fail to test fold change directly. Our research develops a new empirical Bayesian approach to substantially improve the power and accuracy of fold-change detection. Specifically, we more accurately estimate gene-wise error variation in the log of fold change. We then adopt a t-test with adjusted degrees of freedom for significance assessment. We apply our method to a dosage study in Arabidopsis and a Down syndrome study in humans to illustrate the utility of our approach. We also present a simulation study based on real datasets to demonstrate the accuracy of our method relative to error variance estimation and power in fold-change detection. Our developed R package with a detailed user manual is publicly available on GitHub at https://github.com/cuiyingbeicheng/Foldseq.

scholarly journals Synthetic circuit for exact adaptation and fold-change detection

2014 ◽  
Vol 42 (9) ◽  
pp. 6078-6089 ◽  
Author(s):  
Jongmin Kim ◽  
Ishan Khetarpal ◽  
Shaunak Sen ◽  
Richard M. Murray
Keyword(s):  
Change Detection ◽  
Fold Change ◽  
Synthetic Circuit ◽  
Fold Change Detection

scholarly journals Optimal Regulatory Circuit Topologies for Fold-Change Detection

Cell Systems ◽  
2017 ◽  
Vol 4 (2) ◽  
pp. 171-181.e8 ◽  
Author(s):  
Miri Adler ◽  
Pablo Szekely ◽  
Avi Mayo ◽  
Uri Alon
Keyword(s):  
Change Detection ◽  
Fold Change ◽  
Regulatory Circuit ◽  
Fold Change Detection

scholarly journals Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Eugenia Lyashenko ◽  
Mario Niepel ◽  
Purushottam D Dixit ◽  
Sang Kyun Lim ◽  
Peter K Sorger ◽  
...  
Keyword(s):  
Growth Factor ◽  
Change Detection ◽  
Mammalian Cells ◽  
Fold Change ◽  
Analytical Models ◽  
Signaling Networks ◽  
Cell Memory ◽  
Surface Receptor ◽  
Epidermal Growth ◽  
Fold Change Detection

Detecting relative rather than absolute changes in extracellular signals enables cells to make decisions in constantly fluctuating environments. It is currently not well understood how mammalian signaling networks store the memories of past stimuli and subsequently use them to compute relative signals, that is perform fold change detection. Using the growth factor-activated PI3K-Akt signaling pathway, we develop here computational and analytical models, and experimentally validate a novel non-transcriptional mechanism of relative sensing in mammalian cells. This mechanism relies on a new form of cellular memory, where cells effectively encode past stimulation levels in the abundance of cognate receptors on the cell surface. The surface receptor abundance is regulated by background signal-dependent receptor endocytosis and down-regulation. We show the robustness and specificity of relative sensing for two physiologically important ligands, epidermal growth factor (EGF) and hepatocyte growth factor (HGF), and across wide ranges of background stimuli. Our results suggest that similar mechanisms of cell memory and fold change detection may be important in diverse signaling cascades and multiple biological contexts.

scholarly journals Fold-Change Detection of NF-κB at Target Genes with Different Transcript Outputs

2019 ◽  
Vol 116 (4) ◽  
pp. 709-724 ◽  
Author(s):  
Victor C. Wong ◽  
Shibin Mathew ◽  
Ramesh Ramji ◽  
Suzanne Gaudet ◽  
Kathryn Miller-Jensen
Keyword(s):  
Change Detection ◽  
Target Genes ◽  
Fold Change ◽  
Fold Change Detection
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