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

TY - JOUR

T1 - The STRING database in 2011

T2 - functional interaction networks of proteins, globally integrated and scored

AU - Szklarczyk, Damian

AU - Franceschini, Andrea

AU - Kuhn, Michael

AU - Simonovic, Milan

AU - Roth, Alexander

AU - Minguez, Pablo

AU - Doerks, Tobias

AU - Stark, Manuel

AU - Muller, Jean

AU - Bork, Peer

AU - Jensen, Lars J

AU - von Mering, Christian

PY - 2011/1

Y1 - 2011/1

N2 - 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.

AB - 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.

KW - Databases, Protein

KW - Protein Interaction Mapping

KW - Systems Integration

KW - User-Computer Interface

U2 - 10.1093/nar/gkq973

DO - 10.1093/nar/gkq973

M3 - Journal article

C2 - 21045058

SN - 0305-1048

VL - 39

SP - D561-8

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - Database issue

ER -