STRING v10: protein–protein interaction networks, integrated over the tree of life
Damian Szklarczyk,Andrea Franceschini,Stefan Wyder,Kristoffer Forslund,Davide Heller,Jaime Huerta-Cepas,Milan Simonovic,Alexander Roth,Alberto Santos,Kalliopi Tsafou,Michael Kuhn,Peer Bork,Lars Juhl Jensen,Christian von Mering +13 more
TLDR
H hierarchical and self-consistent orthology annotations are introduced for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution in the STRING database.Abstract:
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.read more
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STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk,Annika L. Gable,David Lyon,Alexander Junge,Stefan Wyder,Jaime Huerta-Cepas,Milan Simonovic,Nadezhda Tsankova Doncheva,John H. Morris,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: The latest version of STRING more than doubles the number of organisms it covers, and offers 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.
Journal ArticleDOI
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Damian Szklarczyk,John H. Morris,Helen Cook,Michael Kuhn,Stefan Wyder,Milan Simonovic,Alberto Santos,Nadezhda Tsankova Doncheva,Alexander Roth,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework.
Journal ArticleDOI
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Damian Szklarczyk,Annika L. Gable,Katerina C. Nastou,David Lyon,Rebecca Kirsch,Sampo Pyysalo,Nadezhda Tsankova Doncheva,Marc Legeay,Tao Fang,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: Changes to the text-mining system, a new scoring-mode for physical interactions, as well as extensive user interface features for customizing, extending and sharing protein networks are described.
Journal ArticleDOI
Next-generation characterization of the Cancer Cell Line Encyclopedia
Mahmoud Ghandi,Franklin W. Huang,Franklin W. Huang,Franklin W. Huang,Judit Jané-Valbuena,Judit Jané-Valbuena,Gregory V. Kryukov,Christopher Lo,E. Robert McDonald,Jordi Barretina,Ellen Gelfand,Craig M. Bielski,Haoxin Li,Haoxin Li,Kevin Hu,Alexander Y. Andreev-Drakhlin,Jaegil Kim,Julian M. Hess,Brian J. Haas,François Aguet,Barbara A. Weir,Michael V. Rothberg,Brenton R. Paolella,Michael S. Lawrence,Rehan Akbani,Yiling Lu,Hong L. Tiv,Prafulla C. Gokhale,Antoine de Weck,Ali Amin Mansour,Coyin Oh,Juliann Shih,Kevin Hadi,Yanay Rosen,Jonathan Bistline,Kavitha Venkatesan,Anupama Reddy,Dmitriy Sonkin,Dmitriy Sonkin,Manway Liu,Joseph Lehar,Joshua M. Korn,Dale Porter,Michael D. Jones,Javad Golji,Giordano Caponigro,Jordan E. Taylor,Caitlin M. Dunning,Amanda L. Creech,Allison Warren,James M. McFarland,Mahdi Zamanighomi,Audrey Kauffmann,Nicolas Stransky,Marcin Imielinski,Yosef E. Maruvka,Yosef E. Maruvka,Andrew D. Cherniack,Andrew D. Cherniack,Aviad Tsherniak,Francisca Vazquez,Jacob D. Jaffe,Andrew A. Lane,David M. Weinstock,Cory M. Johannessen,Michael Morrissey,Frank Stegmeier,Robert Schlegel,William C. Hahn,William C. Hahn,Gad Getz,Gordon B. Mills,Jesse S. Boehm,Todd R. Golub,Todd R. Golub,Todd R. Golub,Levi A. Garraway,Levi A. Garraway,William R. Sellers,William R. Sellers +79 more
TL;DR: The original Cancer Cell Line Encyclopedia is expanded with deeper characterization of over 1,000 cell lines, including genomic, transcriptomic, and proteomic data, and integration with drug-sensitivity and gene-dependency data, which reveals potential targets for cancer drugs and associated biomarkers.
Journal ArticleDOI
Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing
Cohorts for Heart,Genetic,Genetic,Genetic,Environmental Risk in Ad,Polygenic Defining Genetic,Perades +6 more
TL;DR: Pathway analysis implicates immunity, lipid metabolism, tau binding proteins, and amyloid precursor protein (APP) metabolism, showing that genetic variants affecting APP and Aβ processing are associated not only with early-onset autosomal dominant Alzheimer’s disease but also with LOAD.
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