Computational protocol: Synergistic Antifungal Activity of Berberine Derivative B-7b and Fluconazole

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Protocol publication

[…] To investigate biological significance, the identified differential proteins in each comparison were input into DAVID bioinformatics resources 6.7 (the Database for Annotation, Visualization, and Integrated Discovery, http://david.abcc.ncifcrf.gov/) for functional annotation and KEGG (the Kyoto Encylopedia of Genes and Genomes) pathway analysis []. Briefly, DAVID functional annotation and KEGG pathway analysis were performed on the list of differential proteins with differential ratio of over ±1.2 and a nominal p-value of less than 0.05 in each comparison. For the Gene Ontology (GO) enrichment in DAVID, the GO terms of “Biological Process”, “Cellular Component” and “Molecular Function” were used, and only the terms that reported a p-value of ≤0.05 and count number ≥5 proteins were selected. The signaling pathways were identified and mapped using DAVID and the KEGG Automatic Annotation Server (KAAS) []. The KEGG pathways with at least 5 proteins and p-value of <0.05 were identified as enriched.Further, protein-protein interaction (PPI) networks of the differential proteins were predicted and analyzed using STRING v9.1 (Search Tool for the Retrieval of Interacting Genes) database []. STRING, a web resource (http://string-db.org/) dedicated to protein-protein interactions including direct (physical) and indirect (functional) associations, quantitatively integrates information from numerous sources including genomic context, high-throughput experiments, (Conserved) co-expression and previous knowledge. Known and predicted protein-protein interactions are scored and integrated, resulting in comprehensive protein networks currently covering 5,214,234 proteins from 1133 organisms in the STRING database. This analysis gave uniquely comprehensive coverage of both experimental and predicted interaction information with a relative confidence score, implying that only interactions with high level of confidence were extracted and considered as valid links for the PPI network [–]. In a given network, proteins are represented as nodes and the interactions are defined as edges (lines), and thicker edges represent stronger associations. For a PPI network, the majority of the nodes were linked with each other, while some of altered proteins were isolated without partners. The “hub” proteins were proteins with a number of edges, meaning the capability of physically interacting with many partners. […]

Pipeline specifications

Software tools DAVID, KAAS
Databases KEGG KEGG PATHWAY
Application Protein interaction analysis
Organisms Cryptococcus neoformans, Candida albicans, Candida tropicalis, Candida parapsilosis, [Candida] glabrata, Homo sapiens
Diseases Mycoses, Drug-Related Side Effects and Adverse Reactions
Chemicals Berberine, Fluconazole