NetworkPainter: dynamic intracellular pathway animation in Cytobank

Karr, Jonathan R.; Guturu, Harendra; Chen, Edward Y.; Blair, Stuart L; Irish, Jonathan M.; Kotecha, Nikesh; Covert, Markus W.

doi:10.1186/s12859-015-0602-4

Cited by 3 publications

(3 citation statements)

References 38 publications

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“…Cl − Ch, Cl − channel; IKBalpha, nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor alpha; IKK, IκB kinase; SGK1, serum/glucocorticoid regulated kinase 1; IL-1β, interleukin-1β; mRNAs, messenger RNAs; NF-κB, nuclear factor kappa B; x, any channel or protein. Figure created using the software Network Painter (Karr et al, 2015). the biphasic Cl − curve towards lower [Cl − ] such that a reduction in the [Cl − ] i increases the expression of JNK and IL-1β-associated responses.…”

Section: CL − As a Signalling Effector For Cftrmentioning

confidence: 99%

The chloride anion as a signalling effector

Valdivieso

Santa‐Coloma

2019

Biological Reviews

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The specific role of the chloride anion (Cl−) as a signalling effector or second messenger has been increasingly recognized in recent years. It could represent a key factor in the regulation of cellular homeostasis. Changes in intracellular Cl− concentration affect diverse cellular functions such as gene and protein expression and activities, post‐translational modifications of proteins, cellular volume, cell cycle, cell proliferation and differentiation, membrane potential, reactive oxygen species levels, and intracellular/extracellular pH. Cl− also modulates functions in different organelles, including endosomes, phagosomes, lysosomes, endoplasmic reticulum, and mitochondria. A better knowledge of Cl− signalling could help in understanding the molecular and metabolic changes seen in pathologies with altered Cl− transport or under physiological conditions. Here we review relevant evidence supporting the role of Cl− as a signalling effector.

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Section: CL − As a Signalling Effector For Cftrmentioning

confidence: 99%

The chloride anion as a signalling effector

Valdivieso

Santa‐Coloma

2019

Biological Reviews

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“…Mass cytometry, although a very recently developed technology , has already begun to have significant impact on molecular, cell and clinical science . It shares many similarities with flow cytometry, in that a mass cytometer is able to perform high‐throughput multiparametric single cell analysis.…”

Section: Introductionmentioning

confidence: 99%

Cell size assays for mass cytometry

2016

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Mass cytometry offers the advantage of allowing the simultaneous measurement of a greater number parameters than conventional flow cytometry. However, to date, mass cytometry has lacked a reliable alternative to the light scatter properties that are commonly used as a cell size metric in flow cytometry (forward scatter intensity—FSC). Here, we report the development of two plasma membrane staining assays to evaluate mammalian cell size in mass cytometry experiments. One is based on wheat germ agglutinin (WGA) staining and the other on Osmium tetroxide (OsO4) staining, both of which have preferential affinity for cell membranes. We first perform imaging and flow cytometry experiments to establish a relationship between WGA staining intensity and traditional measures of cell size. We then incorporate WGA staining in mass cytometry analysis of human whole blood and show that WGA staining intensity has reproducible patterns within and across immune cell subsets that have distinct cell sizes. Lastly, we stain PBMCs or dissociated lung tissue with both WGA and OsO4 ; mass cytometry analysis demonstrates that the two staining intensities correlate well with one another. We conclude that both WGA and OsO4 may be used to acquire cell size-related parameters in mass cytometry experiments, and expect these stains to be broadly useful in expanding the range of parameters that can be measured in mass cytometry experiments.

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“…Actually, there exists some pathway-related studies based on the time-course experiment and data, e.g. a pathway-based phylogenetic approach [24], a web-based software program Network Painter [25], and a new Wnt signaling time-fit model [26]. However, there is still urgent requirement on the computational characterization of interactive pathways and their phenotype-associated states, which should provide a new viewpoint of network of networks for a biological system [27], and should also supply new strategy to state prediction for the phenotype change of a biological system.…”

Section: Introductionmentioning

confidence: 99%

Dynamically characterizing individual clinical change by the steady state of disease-associated pathway

Sun

et al. 2019

BMC Bioinformatics

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BackgroundAlong with the development of precision medicine, individual heterogeneity is attracting more and more attentions in clinical research and application. Although the biomolecular reaction seems to be some various when different individuals suffer a same disease (e.g. virus infection), the final pathogen outcomes of individuals always can be mainly described by two categories in clinics, i.e. symptomatic and asymptomatic. Thus, it is still a great challenge to characterize the individual specific intrinsic regulatory convergence during dynamic gene regulation and expression. Except for individual heterogeneity, the sampling time also increase the expression diversity, so that, the capture of similar steady biological state is a key to characterize individual dynamic biological processes.ResultsAssuming the similar biological functions (e.g. pathways) should be suitable to detect consistent functions rather than chaotic genes, we design and implement a new computational framework (ABP: Attractor analysis of Boolean network of Pathway). ABP aims to identify the dynamic phenotype associated pathways in a state-transition manner, using the network attractor to model and quantify the steady pathway states characterizing the final steady biological sate of individuals (e.g. normal or disease). By analyzing multiple temporal gene expression datasets of virus infections, ABP has shown its effectiveness on identifying key pathways associated with phenotype change; inferring the consensus functional cascade among key pathways; and grouping pathway activity states corresponding to disease states.ConclusionsCollectively, ABP can detect key pathways and infer their consensus functional cascade during dynamical process (e.g. virus infection), and can also categorize individuals with disease state well, which is helpful for disease classification and prediction.

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NetworkPainter: dynamic intracellular pathway animation in Cytobank

Cited by 3 publications

References 38 publications

The chloride anion as a signalling effector

The chloride anion as a signalling effector

Cell size assays for mass cytometry

Dynamically characterizing individual clinical change by the steady state of disease-associated pathway

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