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STRING v9.1: protein-protein interaction networks, with increased coverage and integration

Andrea Franceschini, Damian Szklarczyk, Sune Frankild, Michael Kuhn, Milan Simonovic, Alexander Roth, Jianyi Lin, Pablo Minguez, Peer Bork, Christian von Mering, Lars J. Jensen
2012 Nucleic Acids Research  
Known and predicted associations are scored and integrated, resulting in comprehensive protein networks covering >1100 organisms.  ...  Known and predicted associations are scored and integrated, resulting in comprehensive protein networks covering >1100 organisms.  ...  Yuan (EMBL) for excellent administrative support with the STRING backend servers, and Carlos Garcı´a Giro´n (Sanger Institute) for help in implementing the user-payload-data mechanism.  ... 
doi:10.1093/nar/gks1094 pmid:23203871 pmcid:PMC3531103 fatcat:wtao6pdyyrap5i3kklh52q2m3i

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  ...  Yuan (EMBL Heidelberg) for excellent technical support with the STRING backend servers. Prof.  ... 
doi:10.1093/nar/gku1003 pmid:25352553 pmcid:PMC4383874 fatcat:vnqrdvdswnc6heflo2nqt3uf2y

HAPPI-2: a Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions

Jake Y. Chen, Ragini Pandey, Thanh M. Nguyen
2017 BMC Genomics  
Compared with the HAPPI 1.0 database release, HAPPI database version 2.0 (HAPPI-2) represents a 485% of human PPI data coverage increase and a 73% protein coverage increase.  ...  Human protein-protein interaction (PPI) data is essential to network and systems biology studies.  ...  TN performed the data coverage and quality evaluations, and helped strengthen the research methodology used in this study. All authors read and approved the final manuscript.  ... 
doi:10.1186/s12864-017-3512-1 pmid:28212602 pmcid:PMC5314692 fatcat:5vv4bc7w7jeebgmp2pm7qgyguy

Complete Genome Sequence of Bacillus pumilus Strain WP8, an Efficient Plant Growth-Promoting Rhizobacterium

Yijun Kang, Min Shen, Huanli Wang, Qingxin Zhao
2015 Genome Announcements  
Here, we present the complete genome of WP8 and its genes involved in plant growth promotion and biocontrol.  ...  ACKNOWLEDGMENTS We thank Ye Tao and his colleagues for genome sequencing and analysis at Shanghai Majorbio Bio-pharm Technology Co., Ltd.  ...  Salzberg SL, Delcher AL, Kasif S, White O. 1998. protein interaction networks, with increased coverage and integration. Nucleic Acids Res 41:D808 -D815. http://dx.doi.org/10.1093/ nar/gks1094.  ... 
doi:10.1128/genomea.01452-14 pmid:25614565 pmcid:PMC4319618 fatcat:rqbgrjtegfafdnb44cfykxzaqa

Structural Bioinformatics of the Interactome

Donald Petrey, Barry Honig
2014 Annual Review of Biophysics  
Here we review these techniques, focusing on the construction of physical protein-protein interaction networks, and highlighting approaches that incorporate protein structure which is becoming an increasingly  ...  molecules and how they interact to modulate the behavior of biological systems.  ...  Acknowledgments This work is supported by National Institutes of Health grants GM030518 and GM094597.  ... 
doi:10.1146/annurev-biophys-051013-022726 pmid:24895853 pmcid:PMC4113968 fatcat:xsxg2nc2tjho5f72fn5jgdbdua

Bioinformatics analyses of differentially expressed genes associated with bisphosphonate-related osteonecrosis of the jaw in patients with multiple myeloma

Sun J, Wen X, Jin F, Li Y, Hu J, Sun Y
2015 OncoTargets and Therapy  
Gene ontology (GO) and pathway enrichment analyses of DEGs were performed, followed by functional annotation and proteinprotein interaction network construction.  ...  In proteinprotein interaction network analysis, tumor necrosis factor (TNF) and interleukin 1, beta (IL1B) had higher connectivity degrees.  ...  String v9.1: protein-protein interaction networks, with increased coverage and integration. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T.  ... 
doaj:ca546294a144457380203cd135ca52cc fatcat:u5nrxn4nrbc3rfmsrkydch5c5i

Computational screening of potential glioma-related genes and drugs based on analysis of GEO dataset and text mining

Zhengye Jiang, Yanxi Shi, Guowei Tan, Zhanxiang Wang, Edwin Wang
2021 PLoS ONE  
We also constructed the protein interaction network of common genes through STRING, and selected the important modules for further drug-gene analysis.  ...  Results The gene set obtained from text mining was intersected with the previously obtained DEGs, and 128 common genes were obtained.  ...  STRING v9.1: protein- protein interaction networks, with increased coverage and integration. Nucleic Acids Research. 2013; 41(D1):D808-D15. https://doi.org/10.1093/nar/gks1094 PMID: 23203871 22.  ... 
doi:10.1371/journal.pone.0247612 pmid:33635875 fatcat:52xjjtovybfi3p3t5dqhll7xlu

Arabidopsis proteome responses to the smoke-derived growth regulator karrikin

Jana Baldrianová, Martin Černý, Jan Novák, Petr L. Jedelský, Eva Divíšková, Břetislav Brzobohatý
2015 Journal of Proteomics  
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 2013;41(Database issue):D808-15. Arabidopsis thaliana cells.  ...  Karrikin-responsive genes (TAIR, Nelson and co-workers [8] ; blue) and proteins 17 identified here (brown) were analysed for protein-protein interaction networks.  ... 
doi:10.1016/j.jprot.2015.02.011 pmid:25746380 fatcat:263s7tszfneutiotrc7uoxagwa

Natural Language Processing and Unsupervised Learning: It's Significance on Biomedical Literature

Kanika Gupta, Ashok Kumar
2018 International Journal of Current Research and Review  
Both these approaches can be used to find knowledge from written textual data in the form different interactions like protein-protein, gene-gene, gene-protein, etc.  ...  This information is growing exponentially with the speed exceeding Moore's Law i.e. observations double in every two years.  ...  The authors are also grateful to authors / editors / publishers of all those articles, journals and books from where the literature for this article has been reviewed and discussed.  ... 
doi:10.31782/ijcrr.2018.10143 fatcat:n56phwi4mfa4jkwgutik5r64ze

Mapping the Spatial Proteome of Metastatic Cells in Colorectal Cancer

Marta Mendes, Alberto Peláez-García, María López-Lucendo, Rubén A. Bartolomé, Eva Calviño, Rodrigo Barderas, J. Ignacio Casal
2017 Proteomics  
The protein network organization, protein complexes and functional pathways associated to CRC metastasis was revealed with spatial resolution.  ...  The chaperonin CCT, the Eif2 and Eif3 initiation of translation and the oxidative phosphorylation complexes together with an important number of guanine nucleotidebinding proteins, were deregulated in  ...  ., STRING v9.1: protein-protein interaction networks, with increased coverage and integration.  ... 
doi:10.1002/pmic.201700094 pmid:28861940 fatcat:qoewseenjjczrdrruyayufg2be

Upregulation of Glycolytic Enzymes, Mitochondrial Dysfunction and Increased Cytotoxicity in Glial Cells Treated with Alzheimer's Disease Plasma

Tharusha Jayasena, Anne Poljak, Nady Braidy, George Smythe, Mark Raftery, Mark Hill, Henry Brodaty, Julian Trollor, Nicole Kochan, Perminder Sachdev, Wenhui Hu
2015 PLoS ONE  
A variety of inflammatory markers are increased with the onset of AD pathology, including cytokines and chemokines, coagulation factors and acute-phase reactive proteins as well as reactive astrocytes  ...  Markers of increased protein, lipid and nucleic acid oxidation and reduced activities of antioxidant enzymes have been reported in AD plasma.  ...  cells and Jason Nunes from Proteome Software for his help with the statistical analysis of the proteomics data.  ... 
doi:10.1371/journal.pone.0116092 pmid:25785936 pmcid:PMC4364672 fatcat:exdvbnlsoze2nalxa6pewekigy

Insights into the molecular features of the von Hippel-Lindau like protein [article]

Federica Quaglia, Giovanni Minervini, Francesco Tabaro, Silvio C E Tosatto
2018 bioRxiv   pre-print
Our findings show that VLP may share at least seven interactors with pVHL, suggesting novel functional roles for this under- studied human protein.  ...  Phylogenetic investigation showed VLP to be mostly conserved in upper mammals and specifically expressed in brain and testis.  ...  Conflict of interest and funding  ... 
doi:10.1101/407353 fatcat:6poh6glfqvfzfa2kcrg6o7rejq

Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm

Yunhua Zhang, Li Dai, Ying Liu, YuHang Zhang, ShaoPeng Wang, Quan Zou
2017 PLoS ONE  
Based on validated fruit-related genes, the random walk with restart (RWR) algorithm was applied on a protein-protein interaction (PPI) network using these genes as seeds.  ...  The identified genes with high probabilities were filtered by the permutation test and linkage tests.  ...  STRING v9.1: proteinprotein interaction networks, with increased coverage and integration. Nucleic Acids Research. 2013; 41(Database issue):D808-15.  ... 
doi:10.1371/journal.pone.0177017 pmid:28472169 pmcid:PMC5417634 fatcat:facazucuajgjdivtry2igjwmhm

ProCbA: Protein Function Prediction based on Clique Analysis [article]

Alireza Khanteymoori, Mohammad Bagher Ghajehlo, Soudeh Behrouzinia, Mohammad Hossein Olyaee
2020 bioRxiv   pre-print
Protein function prediction based on protein-protein interactions (PPI) is one of the most important challenges of the Post-Genomic era.  ...  In addition, in ProNC-FA which is not including new algorithm; we try to address the essence of incomplete and noisy data of PPI era in order to achieving a network with complete functional aggregation  ...  In Protein-Protein Networks, with increasing and decreasing the neighborhood degree, the number of proteins is gradually decrease and increase respectively.  ... 
doi:10.1101/2020.11.24.396432 fatcat:supgpfnjgrfirf7u2xyagpbga4

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
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  ...  disrupted protein interactions in the proximity of pathogenic cancer genes.  ...  Franceschini,A. et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res, 41, D808-15.  ... 
doi:10.1101/742379 fatcat:qjpxjczvi5e4lctqdhiz4t77zi
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