Document Type
Article
Source of Publication
Scientific Reports
Publication Date
12-1-2023
Abstract
The signal modelling framework JimenaE simulates dynamically Boolean networks. In contrast to SQUAD, there is systematic and not just heuristic calculation of all system states. These specific features are not present in CellNetAnalyzer and BoolNet. JimenaE is an expert extension of Jimena, with new optimized code, network conversion into different formats, rapid convergence both for system state calculation as well as for all three network centralities. It allows higher accuracy in determining network states and allows to dissect networks and identification of network control type and amount for each protein with high accuracy. Biological examples demonstrate this: (i) High plasticity of mesenchymal stromal cells for differentiation into chondrocytes, osteoblasts and adipocytes and differentiation-specific network control focusses on wnt-, TGF-beta and PPAR-gamma signaling. JimenaE allows to study individual proteins, removal or adding interactions (or autocrine loops) and accurately quantifies effects as well as number of system states. (ii) Dynamical modelling of cell–cell interactions of plant Arapidopsis thaliana against Pseudomonas syringae DC3000: We analyze for the first time the pathogen perspective and its interaction with the host. We next provide a detailed analysis on how plant hormonal regulation stimulates specific proteins and who and which protein has which type and amount of network control including a detailed heatmap of the A.thaliana response distinguishing between two states of the immune response. (iii) In an immune response network of dendritic cells confronted with Aspergillus fumigatus, JimenaE calculates now accurately the specific values for centralities and protein-specific network control including chemokine and pattern recognition receptors.
DOI Link
ISSN
Publisher
Springer Science and Business Media LLC
Volume
13
Issue
1
Disciplines
Computer Sciences | Life Sciences
Keywords
JimenaE, Signal modelling, Boolean networks, Network control
Scopus ID
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Recommended Citation
Kaltdorf, Martin; Breitenbach, Tim; Karl, Stefan; Fuchs, Maximilian; Kessie, David Komla; Psota, Eric; Prelog, Martina; Sarukhanyan, Edita; Ebert, Regina; Jakob, Franz; Dandekar, Gudrun; Naseem, Muhammad; Liang, Chunguang; and Dandekar, Thomas, "Software JimenaE allows efficient dynamic simulations of Boolean networks, centrality and system state analysis" (2023). All Works. 5645.
https://zuscholars.zu.ac.ae/works/5645
Indexed in Scopus
yes
Open Access
yes
Open Access Type
Gold: This publication is openly available in an open access journal/series