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STRING v9.1: protein-protein interaction networks, with increased coverage and integration
2012
Nucleic Acids Research
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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
2014
Nucleic Acids Research
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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
2017
BMC Genomics
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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
2015
Genome Announcements
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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
2014
Annual Review of Biophysics
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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
2015
OncoTargets and Therapy
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Gene ontology (GO) and pathway enrichment analyses of DEGs were performed, followed by functional annotation and protein–protein interaction network construction. ...
In protein–protein 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
2021
PLoS ONE
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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
2015
Journal of Proteomics
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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
2018
International Journal of Current Research and Review
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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
2017
Proteomics
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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
2015
PLoS ONE
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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]
2018
bioRxiv
pre-print
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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
2017
PLoS ONE
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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]
2020
bioRxiv
pre-print
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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]
2019
bioRxiv
pre-print
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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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