Core App: CX JSON file reader and writer. Conclusion: In the treatment of GC, Guishao-Liujun decoction works with a variety of components and targets, establishing the groundwork for further research into its mechanism of action.Copyright © 2022 Qian, Zhang, Xie, Cheng and Cui. databases and their interaction was visualized using, BisoGenet, one of the plugin of. Visualizes enrichments of pathways as an enrichment map, a network representing overlaps among enriched pathways. The MCODE algorithm, one of the Cytoscape plugins, was used to identify highly interconnected sub-networks with parameter settings, including Degree Cutoff2, Node Score Cutoff0.2, K-Core2, and Max. In GC treatment, the KEGG analysis revealed that Guishao-Liujun decoction mainly acted through the tumor necrosis factor (TNF), interleukin 17 (IL-17), and cancer-related signaling pathways, with the best binding performance with TP53, as indicated by the outcomes of macromolecular docking. The STRING and Bisogenet PPI (HPRD database) networks were merged, and the resulted network was used to identify clusters using the MCODE Plug-in. AKT1, TP53, and GO functional analysis were mainly associated with ubiquitination and oxidase reduction activity.
Results: A total of 243 chemical components and 1,448 disease targets including 127 intersecting targets were discovered.
CYTOSCAPE NETWORKS WITH BISOGENET SOFTWARE
The core targets were docked with the active components by the macromolecular docking software application AutoDock Vina. 3.1.3 Core target fishing and protein-protein interaction network construction BisoGenet aims to evaluate the prominence of functional relationships. BisoGenet is a Cytsocape app for gene network building, visualization and analysis. BisoGenet is available at bisogenet-cytoscape/. Biological Network Manager is a Cytoscape plug-in, developed to. This feature facilitates the integration of our software with other tools available in the Cytoscape platform. On the potential target of Guishao-Liujun decoction for GC, gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed using the R-language bioconductor platform, and the outcomes were imported into Cytoscape 3.7.2 software to obtain the KEGG network map. option is provided to allow other networks to be converted to BisoGenet. The obtained targets were imported into Cytoscape 3.7.2 software by using the R language to take the intersection for a Venn analysis to construct active ingredient target networks, and they were imported into the STRING database to construct protein-protein interaction (PPI) networks, with the BisoGenet plugin in Cytoscape 3.7.2 being used for analyzing network topology. Methods: The traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP) and the Traditional Chinese Medicine Integrated Database (TCMID) were used to obtain the chemical composition and targets of all the drugs of Guishao-Liujun decoction, and the targets of GC were screened using GeneCards and Online Mendelian Inheritance in Man (OMIM) databases. Objective: The aim of the study was to use a network pharmacological method to examine the mechanism of Guishao-Liujun decoction against gastric cancer (GC).
CYTOSCAPE NETWORKS WITH BISOGENET PDF
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