Computational protocol: Investigating the Mechanisms of Action of Depside Salt from Salvia miltiorrhiza Using Bioinformatic Analysis

Similar protocols

Protocol publication

[…] On combining the Search Tool for the Retrieval of Interacting Genes (STRING, version 10.0, http://www.string-db.org/, combined score > 0.4) [], Biological General Repository for Interaction Datasets (BioGRID, version 3.4, https://wiki.thebiogrid.org/) [] and Human Protein Reference Database (release 9, http://www.hprd.org/) [] interaction databases, PPI pairs among DSSM-associated genes were predicted. Subsequently, the PPI network was visualised for DSSM-associated genes using the Cytoscape software (http://www.cytoscape.org) []. Using the CytoNCA plug-in [] (version 2.1.6, http://apps.cytoscape.org/apps/cytonca) in Cytoscape, degree centrality (DC), betweenness centrality (BC), and closeness centrality of the nodes were analysed to obtain the hub proteins in the PPI network []. The parameter was set as “without weight.”Based on the MCODE plug-in [] (version 1.4.2; http://apps.cytoscape.org/apps/mcode; parameters set as degree cut-off = 2, maximum depth = 100, node score cut-off = 0.2, and K-core = 2) in Cytoscape, module analysis was conducted for the PPI network. Subsequently, KEGG pathway enrichment analysis was performed for the nodes of significant modules, with FDR < 0.05 as the cut-off criterion. […]

Pipeline specifications

Software tools CytoNCA, MCODE
Databases BioGRID HPRD KEGG PATHWAY
Application Protein interaction analysis
Organisms Salvia miltiorrhiza, Homo sapiens
Diseases Cardiovascular Diseases