scholarly journals An Arabidopsis gene network based on the graphical Gaussian model

2007 ◽  
Vol 17 (11) ◽  
pp. 1614-1625 ◽  
Author(s):  
S. Ma ◽  
Q. Gong ◽  
H. J. Bohnert
2012 ◽  
Vol 6 (1) ◽  
pp. 100 ◽  
Author(s):  
Papapit Ingkasuwan ◽  
Supatcharee Netrphan ◽  
Sukon Prasitwattanaseree ◽  
Morakot Tanticharoen ◽  
Sakarindr Bhumiratana ◽  
...  

2021 ◽  
Author(s):  
Vincent Lau ◽  
Rachel Woo ◽  
Bruno Pereira ◽  
Asher Pasha ◽  
Eddi Esteban ◽  
...  

AbstractGene regulatory networks (GRNs) are complex networks that capture multi-level regulatory events between one or more regulatory macromolecules, such as transcription factors (TFs), and their target genes. Advancements in screening technologies such as enhanced yeast-one-hybrid screens have allowed for high throughput determination of GRNs. However, visualization of GRNs in Arabidopsis has been limited to ad hoc networks and are not interactive. Here, we describe the Arabidopsis GEne Network Tool (AGENT) that houses curated GRNs and provides tools to visualize and explore them. AGENT features include expression overlays, subnetwork motif scanning, and network analysis. We show how to use AGENT’s multiple built-in tools to identify key genes that are involved in flowering and seed development along with identifying temporal multi-TF control of a key transporter in nitrate signaling. AGENT can be accessed at https://bar.utoronto.ca/AGENT.


2020 ◽  
Author(s):  
M. Annelise Blanchard ◽  
isabelle roskam ◽  
Moïra Mikolajczak ◽  
Alexandre Heeren

Background: The use of network analyses in psychology has increasingly gained traction in the last few years. A network perspective views psychological constructs as dynamic systems of interacting elements. Objective: We present the first study to apply network analyses to examine how the hallmark features of parental burnout — i.e., exhaustion related to the parental role, emotional distancing from children, and a sense of ineffectiveness in the parental role — interact with one another and with maladaptive behaviors related to the partner and the child(ren), when these variables are conceptualized as a network system. Participants and setting: In a preregistered fashion, we reanalyzed the data from a French-speaking sample (n = 1551; previously published in Mikolajczak, Brianda, Avalosse, & Roskam, 2018), focusing on seven specific variables: the three hallmark parental burnout features, partner conflict, partner estrangement, neglectful behavior toward children, and violent behavior toward children. Methods: We computed two types of network models, a graphical Gaussian model to examine network structure, potential communities, and influential nodes, and a directed acyclic graph to examine the probabilistic dependencies among the different variables. Results: Both network models pointed to emotional distance as an especially potent mechanism in activating all other nodes. Conclusions: These results suggest emotional distance as critical to the maintenance of the parental burnout network and a prime candidate for future interventions, while affirming that network analysis can successfully expose the structure and relationship of variables related to parental burnout and its consequences related to the partner and the child(ren).


Author(s):  
Ahmad Borzou ◽  
Rovshan G Sadygov

Abstract Motivation Inferring the direct relationships between biomolecules from omics datasets is essential for the understanding of biological and disease mechanisms. Gaussian Graphical Model (GGM) provides a fairly simple and accurate representation of these interactions. However, estimation of the associated interaction matrix using data is challenging due to a high number of measured molecules and a low number of samples. Results In this article, we use the thermodynamic entropy of the non-equilibrium system of molecules and the data-driven constraints among their expressions to derive an analytic formula for the interaction matrix of Gaussian models. Through a data simulation, we show that our method returns an improved estimation of the interaction matrix. Also, using the developed method, we estimate the interaction matrix associated with plasma proteome and construct the corresponding GGM and show that known NAFLD-related proteins like ADIPOQ, APOC, APOE, DPP4, CAT, GC, HP, CETP, SERPINA1, COLA1, PIGR, IGHD, SAA1 and FCGBP are among the top 15% most interacting proteins of the dataset. Availability and implementation The supplementary materials can be found in the following URL: http://dynamic-proteome.utmb.edu/PrecisionMatrixEstimater/PrecisionMatrixEstimater.aspx. Supplementary information Supplementary data are available at Bioinformatics online.


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