STRINGdb

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

• Version: 2.24.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Imports: png, sqldf, plyr, igraph, httr, RColorBrewer, gplots, hash, plotrix
• System requirements: URL
• Install: BiocManager::install("STRINGdb")

When to Use

• Mapping a list of differentially expressed genes to STRING database identifiers using the map method.
• Computing functional enrichment (e.g., Gene Ontology, KEGG) for a set of proteins using get_enrichment.
• Visualizing protein-protein interaction networks with custom node colors based on log fold-change using add_diff_exp_color and plot_network.
• Retrieving specific interaction partners and experimental evidence scores for proteins of interest using get_interaction_partners.
• Extracting network clusters/communities from a mapped dataset using get_clusters.

When NOT to Use

• For offline network analysis with custom, non-STRING interaction networks, use igraph instead because STRINGdb is designed to query the online STRING database.
• For primary differential expression analysis of microarray data, use limma instead because STRINGdb requires pre-analyzed differential expression results (e.g., p-values and log fold changes).

Data Requirements

• A data frame containing gene identifiers (e.g., HUGO names, Entrez GeneID, ENSEMBL proteins) and optional numeric columns like pvalue or logFC.
• NCBI taxonomy identifiers for the organism of interest (e.g., 9606 for Human, 10090 for Mouse).