STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

Abstract

Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein–protein associations is incomplete and exhibits varying levels of annotation granularity and reliability. The STRING database aims to collect, score and integrate all publicly available sources of protein–protein interaction information, and to complement these with computational predictions. Its goal is to achieve a comprehensive and objective global network, including direct (physical) as well as indirect (functional) interactions. The latest version of STRING (11.0) more than doubles the number of organisms it covers, to 5090. The most important new feature is an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. For the enrichment analysis, STRING implements well-known classification systems such as Gene Ontology and KEGG, but also offers additional, new classification systems based on high-throughput text-mining as well as on a hierarchical clustering of the association network itself. The STRING resource is available online at https://string-db.org/.

The establishment of immune infiltration based novel recurrence predicting nomogram in prostate cancer

“…ROC and AUC were completed to assess the discriminatory ability of the nomogram, while decision curve analysis was also performed to evaluate the usability of the nomogram. STRING, an online tool that could reveal the functional protein association networks, was employed to identify androgen receptor associated proteins . All analyses were conducted using R version 3.5.3.…”

The Tumor Suppressor SCRIB is a Negative Modulator of the Wnt/β‐Catenin Signaling Pathway

“…Interaction network were generated using STRING's website (version 11.0) at high confidence (0.7) and network is clustered using a Markov Clustering algorithm “MCL inflation parameter = 3” (https://string-db.org/). BioGRID version 3.5.171 was used to extract known SCRIB and LANO interactors . The MS proteomics data, including search results, were deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD013636 and PXD013647.…”

LncRNA‐SULT1C2A regulates Foxo4 in congenital scoliosis by targeting rno‐miR‐466c‐5p through PI3K‐ATK signalling

“…From the STRING database, the protein interaction and correlation score between Foxo4 and AKT1 was 0.984, and as a substrate of the PI3K‐AKT pathway, we selected this interaction as the target. The AKT, p‐AKT and PI3K (p85 regulatory subunit) expression levels were measured via western blot analysis.…”