TY - JOUR
T1 - STRING v10
T2 - protein-protein interaction networks, integrated over the tree of life
AU - Szklarczyk, Damian
AU - Franceschini, Andrea
AU - Wyder, Stefan
AU - Forslund, Kristoffer
AU - Heller, Davide
AU - Huerta-Cepas, Jaime
AU - Simonovic, Milan
AU - Roth, Alexander
AU - Santos Delgado, Alberto
AU - Tsafou, Kalliopi P
AU - Kuhn, Michael
AU - Bork, Peer
AU - Jensen, Lars J
AU - von Mering, Christian
N1 - © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2015/1/28
Y1 - 2015/1/28
N2 - The many functional partnerships and interactions that occur between proteins are at the core of cellular processing and their systematic characterization helps to provide context in molecular systems biology. However, known and predicted interactions are scattered over multiple resources, and the available data exhibit notable differences in terms of quality and completeness. The STRING database (http://string-db.org) aims to provide a critical assessment and integration of protein-protein interactions, including direct (physical) as well as indirect (functional) associations. The new version 10.0 of STRING covers more than 2000 organisms, which has necessitated novel, scalable algorithms for transferring interaction information between organisms. For this purpose, we have introduced hierarchical and self-consistent orthology annotations for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution. Further improvements in version 10.0 include a completely redesigned prediction pipeline for inferring protein-protein associations from co-expression data, an API interface for the R computing environment and improved statistical analysis for enrichment tests in user-provided networks.
AB - The many functional partnerships and interactions that occur between proteins are at the core of cellular processing and their systematic characterization helps to provide context in molecular systems biology. However, known and predicted interactions are scattered over multiple resources, and the available data exhibit notable differences in terms of quality and completeness. The STRING database (http://string-db.org) aims to provide a critical assessment and integration of protein-protein interactions, including direct (physical) as well as indirect (functional) associations. The new version 10.0 of STRING covers more than 2000 organisms, which has necessitated novel, scalable algorithms for transferring interaction information between organisms. For this purpose, we have introduced hierarchical and self-consistent orthology annotations for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution. Further improvements in version 10.0 include a completely redesigned prediction pipeline for inferring protein-protein associations from co-expression data, an API interface for the R computing environment and improved statistical analysis for enrichment tests in user-provided networks.
U2 - 10.1093/nar/gku1003
DO - 10.1093/nar/gku1003
M3 - Journal article
C2 - 25352553
VL - 43
SP - D447-52
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - D1
ER -