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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 P. Tsafou, Michael Kuhn, Peer Bork (+2 others)
2014 Nucleic Acids Research  
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 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  ...  ACKNOWLEDGMENTS The authors wish to thank Yan P. Yuan (EMBL Heidelberg) for excellent technical support with the STRING backend servers. Prof.  ... 
doi:10.1093/nar/gku1003 pmid:25352553 pmcid:PMC4383874 fatcat:vnqrdvdswnc6heflo2nqt3uf2y

PPInfer: a Bioconductor package for inferring functionally related proteins using protein interaction networks

Dongmin Jung, Xijin Ge
2017 F1000Research  
.: STRING v10: proteinprotein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015; 41(Database issue): D447-52. PubMed Abstract | Publisher Full Text | Free Full Text 3.  ...  This fact has motivated the development of a variety of experimental methods for the identification of protein-protein interaction (PPI) networks.  ...  How do these proteins functionally interact with the ras pathway proteins in the STRING network? Perhaps you could discuss the STRING confidence scores or types of evidence for these interactions.  ... 
doi:10.12688/f1000research.12947.1 fatcat:2djxc54sbjhdnaxwiweim774am

MNNG-Regulated Differentially Expressed Genes that Contribute to Cancer Development in Stomach Cells

Tae-Jin Kim, Myeong-Kwan Kim, Dongju Jung
2021 Korean Journal of Clinical Laboratory Science  
STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res.  ...  Protein-protein interaction (PPI) network analyses using the STRING database for the DEGs expressed in the cancer cells.  ... 
doi:10.15324/kjcls.2021.53.4.353 fatcat:t5gb2n66n5h2pesb2avtcuxhei

Pathway and network embedding methods for prioritizing psychiatric drugs [article]

Yash Pershad, Margaret Guo, Russ B Altman
2019 bioRxiv   pre-print
Using protein-protein- interaction networks and embedding-based methods, we build a pipeline to prioritize treatments for psychiatric diseases that achieves a 3.4-fold improvement over a background model  ...  Extensive evidence implicates genetic factors and signaling disruption in the pathophysiology of these diseases.  ...  STRING v10 PPI network (String) 37 and included the genes along each path in a larger disease module.  ... 
doi:10.1101/728055 fatcat:6qa7h5e6sjcjlfvvmupztwm3ey

PPInfer: a Bioconductor package for inferring functionally related proteins using protein interaction networks

Dongmin Jung, Xijin Ge
2017 F1000Research  
Szklarczyk D, Franceschini A, Wyder S, et al.: STRING v10: proteinprotein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015; 41(Database issue): D447-52.  ...  This fact has motivated the development of a variety of experimental methods for the identification of protein-protein interaction (PPI) networks.  ...  network for high-confidence protein interactions of the Ras pathway and top 20 proteins is drawn by STRING.  ... 
doi:10.12688/f1000research.12947.2 fatcat:th6esryu5fazrbzp6xmh4cz3r4

An integrative machine learning approach for prediction of toxicity-related drug safety [article]

Artem Lysenko, Alok Sharma, Keith Boroevich, Tatsuhiko Tsunoda
2018 bioRxiv   pre-print
Computational methods capable of predicting these failures can reduce waste of resources and time devoted to the investigation of compounds that ultimately fail.  ...  Unacceptable drug toxicity is a substantial cause of drug failure during clinical trials as well as the leading cause of drug withdraws after release to market.  ...  Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP: STRING v10: protein-protein interaction networks, integrated over the tree of life  ... 
doi:10.1101/455667 fatcat:z4yubkrwlbe4vn337zssd7usbm

A computationally engineered RAS rheostat reveals RAS–ERK signaling dynamics

John C Rose, Po-Ssu Huang, Nathan D Camp, Jordan Ye, Andrew M Leidal, Inna Goreshnik, Bridget M Trevillian, Miles S Dickinson, Daniel Cunningham-Bryant, Jayanta Debnath, David Baker, Alejandro Wolf-Yadlin (+1 others)
2016 Nature Chemical Biology  
STRING v10: protein--protein interaction networks, integrated over the tree of life. Nucleic Acids Research 43, D447-52 (2015). 2. Wang, J., Duncan, D., Shi, Z. & Zhang, B.  ...  Class II phosphosites derive from a highly interconnected protein interaction network. STRING interaction network of proteins represented by Class II phosphosites.  ... 
doi:10.1038/nchembio.2244 pmid:27870838 pmcid:PMC5161653 fatcat:zqmfmjaiozdodjekkjii6hljfy

Study on cocoonase, sericin, and degumming of silk cocoon: computational and experimental

Preeti Anand, Jay Prakash Pandey, Dev Mani Pandey
2021 Journal of Genetic Engineering and Biotechnology  
California, San Francisco (UCSF) Chimera, and Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) were used for characterization of cocoonase and sericin proteins.  ...  as their interaction with other proteins.  ...  However, no functional interacting network of sericin (BAD00699.1) protein with other protein was predicted by STRING v10.  ... 
doi:10.1186/s43141-021-00125-2 pmid:33594479 fatcat:omgnx7j6xbhg7j6kapzly6sxva

Cerebrospinal Fluid Biomarkers of Japanese Encephalitis

Nabonita Sengupta, Sriparna Mukherjee, Piyush Tripathi, Rashmi Kumar, Amol Ratnakar Suryawanshi, Anirban Basu
2015 F1000Research  
Szklarczyk D, Franceschini A, Wyder S, et al.: STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015; 43(Database issue): D447-452.  ...  Kew RR, Webster RO: Gc-globulin (vitamin D-binding protein) enhances the neutrophil chemotactic activity of C5a and C5a des Arg. J Clin Invest. 1988; 82(1): 364-369.  ...  Acknowledgements The authors would like to acknowledge the kind help provided by R. Rajendra Kumar Reddy, Central Proteomics Facility at Institute of Life Sciences, Bhubaneswar, India.  ... 
doi:10.12688/f1000research.6801.2 fatcat:vnl53srxizdfnl7r2mrzhgtsnu

Databases and tools for constructing signal transduction networks in cancer

Seungyoon Nam
2017 BMB Reports  
Most network generation tools are based on whole transcriptome data. Using statistical models, the integration of other data types into network topology is still challenging.  ...  One of the representative applications of systems biology is to generate a biological network from high-throughput big data, providing a global map of molecular events associated with specific phenotype  ...  Szklarczyk D, Franceschini A, Wyder S et al (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 43, D447-452 32.  ... 
doi:10.5483/bmbrep.2017.50.1.135 pmid:27502015 pmcid:PMC5319659 fatcat:pwjpj6my6bblzj6lcu4urbxxkm

Pathogenic impact of isoform switches in 1209 cancer samples covering 27 cancer types using an isoform-specific interaction network [article]

Abdullah Kahraman, Christian von Mering
2019 bioRxiv   pre-print
disrupted protein interactions in the proximity of pathogenic cancer genes.  ...  To address these questions, we have developed CanIsoNet, a novel isoform-specific protein-protein interaction network that identifies binding domain losses and interaction disruptions in known alternatively  ...  D. et al. (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res., 43, D447-D452. Interactome networks and human disease. Cell, 144, 986-998.  ... 
doi:10.1101/742379 fatcat:qjpxjczvi5e4lctqdhiz4t77zi

PPInfer: a Bioconductor package for inferring functionally related proteins using protein interaction networks

Dongmin Jung, Xijin Ge
2018 F1000Research  
Szklarczyk D, Franceschini A, Wyder S, et al.: STRING v10: proteinprotein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015; 43(Database issue): D447-52.  ...  This fact has motivated the development of a variety of experimental methods for the identification of protein-protein interaction (PPI) networks.  ...  network for high-confidence protein interactions of the RAS pathway and top 20 proteins is drawn by STRING.  ... 
doi:10.12688/f1000research.12947.3 fatcat:iaklynwuhzhytptbwf4iq5u5dq

Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways

Vikram Khurana, Jian Peng, Chee Yeun Chung, Pavan K. Auluck, Saranna Fanning, Daniel F. Tardiff, Theresa Bartels, Martina Koeva, Stephen W. Eichhorn, Hadar Benyamini, Yali Lou, Andy Nutter-Upham (+18 others)
2017 Cell Systems  
Graphical Abstract Highlights d 332 modifiers of a-syn toxicity in yeast are assembled in a gene network d The computational method TransposeNet transposes molecular interactions across species d A "humanized  ...  Modifiers from genome-wide screens against alphasynuclein toxicity in yeast yield a "humanized" network that interconnects genetic forms of parkinsonism and predicts pathologies in patient-derived neurons  ...  ., and S.L. are scientific co-founders of Yumanity Therapeutics, a company developing neurodegenerative disease therapeutics.  ... 
doi:10.1016/j.cels.2016.12.011 pmid:28131822 pmcid:PMC5388136 fatcat:temccumfpnfs5heg5ndjd7zoae

A scored human protein-protein interaction network to catalyze genomic interpretation [article]

Taibo Li, Rasmus Wernersson, Rasmus Borup Hansen, Heiko Horn, Johnathan M Mercer, Greg Slodkowicz, Christopher Workman, Olga Regina, Kristoffer Rapacki, Hans-Henrik Staerfeldt, Soren Brunak, Thomas S Jensen (+1 others)
2016 bioRxiv   pre-print
We describe a general computational framework that through data integration and quality control provides a scored human protein-protein interaction network (InWeb_IM).  ...  Human protein-protein interaction networks are critical to understanding cell biology and interpreting genetic and genomic data, but are challenging to produce in individual large-scale experiments.  ...  Acknowledgements The authors would like to thank Louis Wich for developing the graphical user interface for  ... 
doi:10.1101/064535 fatcat:6ijagl6b35gixnnst2lvhgxdna

Pathway and network embedding methods for prioritizing psychiatric drugs

Yash Pershad, Margaret Guo, Russ B Altman
2020 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
Using protein-protein-interaction networks and embedding-based methods, we build a pipeline to prioritize treatments for psychiatric diseases that achieves a 3.4-fold improvement over a background model  ...  Extensive evidence implicates genetic factors and signaling disruption in the pathophysiology of these diseases.  ...  Our code is available at https://github.com/ypershad/pathway-network-psych-drugs.  ... 
pmid:31797637 pmcid:PMC6951442 fatcat:7dyk34uslzgk5imwu6nnumedki
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