The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest

The paper describes the 2023 release of the STRING database, which systematically collects and integrates protein-protein interactions, covering both direct physical interactions and broader functional associations. Its data come from automated text mining of the literature, computational predictions from co-expression and conserved genomic context, databases of interaction experiments, and curated complexes and pathways; all interactions are critically assessed, scored, and automatically transferred to less well-studied organisms using hierarchical orthology information, and can be accessed via the website, programmatically, or through bulk downloads.

The major additions in version 12.0 are the ability to create, browse, and analyze a full interaction network for any novel genome by submitting its complement of encoded proteins; a co-expression channel that now uses variational autoencoders and incorporates single-cell RNA-seq and experimental proteomics data; and confidence estimates for each experimentally derived interaction based on the detection method used. STRING also extended its functional enrichment analysis so that it is fully available for user-submitted genomes, broadening the resource's usefulness across newly sequenced organisms.