STRING v10: protein–protein interaction networks, integrated over the tree of life

STRING v10: protein–protein interaction networks, integrated over the tree of life

2014 | Damian Szklarczyk¹, Andrea Franceschini¹, Stefan Wyder¹, Kristoffer Forslund², Davide Heller¹, Jaime Huerta-Cepas², Milan Simonovic¹, Alexander Roth¹, Alberto Santos³, Kalliopi P. Tsafou³, Michael Kuhn⁴,⁵, Peer Bork²,*, Lars J. Jensen³,*, and Christian von Mering¹,*
STRING v10 is a comprehensive database that integrates protein-protein interaction (PPI) data across the tree of life. It provides a critical assessment and integration of both direct and indirect interactions, including experimental and predicted associations. The database covers over 2000 organisms, requiring new algorithms for transferring interaction information between species. STRING v10 introduces hierarchical and self-consistent orthology annotations, grouping proteins into phylogenetic families. It also features a redesigned prediction pipeline for co-expression data, an API for R, and improved statistical analysis for enrichment tests. The database focuses on functional associations between proteins, integrating all types of interactions, such as stable physical associations, transient binding, and signaling. STRING is one of several online resources that aim to provide comprehensive PPI data. It emphasizes interaction confidence scoring, comprehensive coverage, and user-friendly interfaces. The main entry point is a protein search box that allows queries for multiple proteins and restricts searches to specific organisms. STRING provides a network view where users can inspect interaction evidence, adjust score-cutoffs, and view detailed protein information. The 'advanced' mode allows clustering and rearranging networks and testing for statistical enrichments, including human disease associations and tissue annotations. STRING connects with partner databases like TISSUES and DISEASES for these annotations. Interaction transfer between organisms is based on orthology relations, with STRING v10 using a post-processing pipeline to ensure self-consistent orthology assignments. Co-expression analysis in STRING v10 uses an improved pipeline, incorporating data from NCBI GEO, leading to better benchmark performance. The database also offers access via a REST API and R/Bioconductor, allowing users to analyze and visualize networks, and perform statistical enrichment tests on gene lists. STRING v10 enhances the integration of PPI data, providing a global view of protein interactions and supporting advanced analysis tools for researchers in functional genomics and systems biology.STRING v10 is a comprehensive database that integrates protein-protein interaction (PPI) data across the tree of life. It provides a critical assessment and integration of both direct and indirect interactions, including experimental and predicted associations. The database covers over 2000 organisms, requiring new algorithms for transferring interaction information between species. STRING v10 introduces hierarchical and self-consistent orthology annotations, grouping proteins into phylogenetic families. It also features a redesigned prediction pipeline for co-expression data, an API for R, and improved statistical analysis for enrichment tests. The database focuses on functional associations between proteins, integrating all types of interactions, such as stable physical associations, transient binding, and signaling. STRING is one of several online resources that aim to provide comprehensive PPI data. It emphasizes interaction confidence scoring, comprehensive coverage, and user-friendly interfaces. The main entry point is a protein search box that allows queries for multiple proteins and restricts searches to specific organisms. STRING provides a network view where users can inspect interaction evidence, adjust score-cutoffs, and view detailed protein information. The 'advanced' mode allows clustering and rearranging networks and testing for statistical enrichments, including human disease associations and tissue annotations. STRING connects with partner databases like TISSUES and DISEASES for these annotations. Interaction transfer between organisms is based on orthology relations, with STRING v10 using a post-processing pipeline to ensure self-consistent orthology assignments. Co-expression analysis in STRING v10 uses an improved pipeline, incorporating data from NCBI GEO, leading to better benchmark performance. The database also offers access via a REST API and R/Bioconductor, allowing users to analyze and visualize networks, and perform statistical enrichment tests on gene lists. STRING v10 enhances the integration of PPI data, providing a global view of protein interactions and supporting advanced analysis tools for researchers in functional genomics and systems biology.
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Understanding STRING v10%3A protein%E2%80%93protein interaction networks%2C integrated over the tree of life