The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

Abstract

An essential prerequisite for any systems-level understanding of cellular functions is to correctly uncover and annotate all functional interactions among proteins in the cell. Toward this goal, remarkable progress has been made in recent years, both in terms of experimental measurements and computational prediction techniques. However, public efforts to collect and present protein interaction information have struggled to keep up with the pace of interaction discovery, partly because protein–protein interaction information can be error-prone and require considerable effort to annotate. Here, we present an update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING); it provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information. Interactions in STRING are provided with a confidence score, and accessory information such as protein domains and 3D structures is made available, all within a stable and consistent identifier space. New features in STRING include an interactive network viewer that can cluster networks on demand, updated on-screen previews of structural information including homology models, extensive data updates and strongly improved connectivity and integration with third-party resources. Version 9.0 of STRING covers more than 1100 completely sequenced organisms; the resource can be reached at http://string-db.org.

Vaccinia Virus Infection Requires Maturation of Macropinosomes

“…Thirty‐three cell factors fulfilled the criteria (Figure 2A and Table S2). When the hits were clustered using our network visualization algorithm 42, which takes in account physical interactions defined in string 49 and cellular functions annotated in david 50, 51, we found that the hits fell into six clusters: membrane trafficking, Rab conversion, endosomal positioning and acidification, PI metabolism and the regulation of actin (Figure 2A and Table S2).…”

Resilience of death: intrinsic disorder in proteins involved in the programmed cell death

“…Figure 7 represents the PONDR-FIT disorder profiles of three human proteins known to be involved in p53-mediated apoptotic signaling pathway, and also shows the results of the functional analysis of these proteins using the STRING database. 39 This database acts as a 'one-stop shop' for all information on functional links between proteins, and version 9.0 of STRING (accessible at http://string-db.org) covers 41100 completely sequenced organisms, including Homo Figure S1. Figure 7 and Supplementary Figure S1 show that all the members of the p53-controlled apoptosis signaling pathway are involved in multiple interactions and therefore can be considered as hub proteins.…”

“…STRING database is the online database resource Search Tool for the Retrieval of Interacting Genes, which provides both experimental and predicted interaction information. 39 For each protein, STRING produces the network of predicted associations for a particular group of proteins. The network nodes are proteins.…”

“…The edges represent the functional associations evaluated based on the experiments, search of databases and text mining. The thickness of edges is proportional to the confidence level 39 p53, which possesses functionally important IDPRs. 40,41 Here, B70% of the interactions of p53 are mediated by IDPRs containing 86, 90, and 100% of observed acetylation, phosphorylation, and protein conjugation sites of this protein, respectfully.…”

Drug Repurposing by Simulating Flow Through Protein–Protein Interaction Networks

“…The list of protein–protein interactions was downloaded from the STRING 9.0 database 37. Highly reliable (confidence score greater than 0.800) directed interactions available for Homo sapiens with known action (i.e., activation or inhibition) were used for protein–protein interaction network construction.…”