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STRING 8--a global view on proteins and their functional interactions in 630 organisms

L. J. Jensen, M. Kuhn, M. Stark, S. Chaffron, C. Creevey, J. Muller, T. Doerks, P. Julien, A. Roth, M. Simonovic, P. Bork, C. von Mering
2009 Nucleic Acids Research  
Version 8.0 of STRING covers about 2.5 million proteins from 630 organisms, providing the most comprehensive view on protein-protein interactions currently available.  ...  STRING is a database and web resource dedicated to protein-protein interactions, including both physical and functional interactions.  ...  ACKNOWLEDGEMENTS The authors wish to thank Dianna Fisk from the Saccharomyces Genome Database, and Thomas B. Brody from The Interactive Fly, for access to gene summary paragraphs.  ... 
doi:10.1093/nar/gkn760 pmid:18940858 pmcid:PMC2686466 fatcat:nhfdvr3ycfhfnfswksdthtolai

Comparative Network Analysis of Two-Component Signal Transducing Protein-Protein Interactions in Enterococcus faecalis Sp

Ranjith N. Kumavath
2012 Journal of Proteomics & Bioinformatics  
Protein-Protein interactions network analysis of Enterococcus faecalis sp. in a comparative approach helps for the dissection of gene function, potential signal transduction, and virulence pathways.  ...  prediction analysis and Host-Pathogen Interactions analysis using STRING and HPIDB databases.  ...  of node degree and topological coefficient; the distribution of protein category and PPI; conserved subnetworks; protein-protein interactions pairs of Enterococcus faecalis; are available as a supporting  ... 
doi:10.4172/jpb.1000249 fatcat:vp7zyr7qojgfld2nercyr6o24i

Identification and validation of circulating miRNAs as potential new biomarkers for severe liver disease in patients with leptospirosis

Natthaya Chuaypen, Umaporn Limothai, Pattapon Kunadirek, Pornchai Kaewsapsak, Patipark Kueanjinda, Nattachai Srisawat, Pisit Tangkijvanich, Yun Zheng
2021 PLoS ONE  
On regression analysis, elevated miR-601 and miR-630 expression were also predictive of multi-organ failures and poor overall survival.  ...  Leptospirosis, a global zoonotic infectious disease, has various clinical manifestations ranging from mild self-limiting illness to life-threatening with multi-organ damage, including liver involvement  ...  Acknowledgments We gratefully thank the members of Center of Excellence in Hepatitis and Liver Cancer, Faculty of Medicine, Chulalongkorn University for their valuable suggestions and help.  ... 
doi:10.1371/journal.pone.0257805 pmid:34570814 pmcid:PMC8476044 fatcat:t4igmzpy4jdanjcqbgpw2zmbai

Predicting Protein Phenotypes Based on Protein-Protein Interaction Network

Lele Hu, Tao Huang, Xiao-Jun Liu, Yu-Dong Cai, Hitoshi Okazawa
2011 PLoS ONE  
Methodology/Principal Findings: Here, we proposed a new method for predicting protein phenotypes in yeast based on protein-protein interaction network.  ...  In addition, the method can be easily applied to the prediction of protein associated phenotypes in other organisms.  ...  M, Chaffron S, Creevey C, et al. (2009) STRING 8-a global view on proteins and their functional interactions in 630 organisms.  ... 
doi:10.1371/journal.pone.0017668 pmid:21423698 pmcid:PMC3053377 fatcat:gr6xprbuajc3jgeoesweabmwd4

Predicting Functions of Proteins in Mouse Based on Weighted Protein-Protein Interaction Network and Protein Hybrid Properties

Lele Hu, Tao Huang, Xiaohe Shi, Wen-Cong Lu, Yu-Dong Cai, Kuo-Chen Chou, Christos Ouzounis
2011 PLoS ONE  
In view of this, a new approach is proposed by hybridizing the PPI information and the biochemical/physicochemical features of protein sequences.  ...  Methodology/Principal Findings: Although many efforts have been made in this regard, most of them were based on either sequence similarity or protein-protein interaction (PPI) information.  ...  Acknowledgments We thank MfunGD, STRING and IntAct for supply data to support notfor-profit research efforts. Author Contributions  ... 
doi:10.1371/journal.pone.0014556 pmid:21283518 pmcid:PMC3023709 fatcat:2pd3paaw2jdzxmahjceunmc27i

Elucidating the genome of Emydura subglobosa through manual annotation and computational biology tools [article]

Megan R Yu
2021 bioRxiv   pre-print
Through functional, localization, and structural analyses of the predicted proteins, we have discovered conserved genes encoding proteins that play a role in C21-steroid hormone biosynthetic processes,  ...  However, automated technologies often result in a high frequency of errors through the process of assembly and annotation and highlight the need for manual annotation.  ...  Acknowledgements 783 Thank you to Professor Matteo Pellegrini, Leroy Bondhus, and Noah Alexander for their 784 teaching and guidance throughout MCD BIO 187AL. 785  ... 
doi:10.1101/2021.06.24.449536 fatcat:wdymo4pyergsdatz7saggqgkum

High accuracy operon prediction method based on STRING database scores

Blanca Taboada, Cristina Verde, Enrique Merino
2010 Nucleic Acids Research  
by STRING database (Jensen,L.J., Kuhn,M., Stark,M., Chaffron,S., Creevey,C., Muller,J., Doerks,T., Julien,P., Roth,A., Simonovic,M. et al. (2009) STRING 8-a global view on proteins and their functional  ...  interactions in 630 organisms.  ...  ACKNOWLEDGEMENTS We thank Shirley Ainsworth for bibliographical assistance, Ricado Ciria, Juan Manuel Hurtado, Arturo Ocadiz, Alma Martinez and Abel Linares for computer support and Maria Luisa Tabche  ... 
doi:10.1093/nar/gkq254 pmid:20385580 pmcid:PMC2896540 fatcat:f5taehnbfzan5cjadfix543ckm

Insights into archaeal chaperone machinery: a network-based approach

Shikha Rani, Ankush Sharma, Manisha Goel
2018 Cell stress & chaperones (Print)  
Very few studies have been ventured into system-level analysis of chaperones and their functioning in archaeal cells.  ...  Molecular chaperones are a diverse group of proteins that ensure proteome integrity by helping the proteins fold correctly and maintain their native state, thus preventing their misfolding and subsequent  ...  Acknowledgements We are thankful to the reviewers for appreciating the work we have done and for providing detailed and constructive suggestions.  ... 
doi:10.1007/s12192-018-0933-y pmid:30178307 pmcid:PMC6237683 fatcat:ys6uurhyjrbmvkw26shb4m67uu

Network systems biology for targeted cancer therapies

Ting-Ting Zhou
2012 Chinese Journal of Cancer  
It has also introduced great changes into the research paradigm of cancer鄄 associated drug discovery and drug resistance.  ...  From biological network modeling to structural/dynamic network analysis, network systems biology provides unique insight into the potential mechanisms underlying the growth and progression of cancer cells  ...  It contains interactions for over 74 000 small molecules and over 2.5 million proteins in 630 organisms. Contains data of drugs, proteins, and side effects, as well as relations between them.  ... 
doi:10.5732/cjc.011.10282 pmid:22176777 pmcid:PMC3777487 fatcat:hidrfb3p4bcthlrq7x2h4knpxu

An Anthropological review on COVID-19 and its Reflection in Indian Demography

Debashmita Banerjee
2020 International Journal for Research in Applied Science and Engineering Technology  
COVID-19 pandemic is a global issue and the morbidity is increasing day by day.  ...  A specific species of it was widespread from China (SARS-CoV-2) on the late December 2019 and nowadays different countries were in its trap.  ...  The C and N-terminal has specific functional orientation. On one hand C-terminal interacts with M protein and N -terminal reacts with the membrane of host cells.  ... 
doi:10.22214/ijraset.2020.6374 fatcat:pdpdyeubzbeevictfdxctjnh7m

Construction and analysis of the protein-protein interaction network related to essential hypertension

Jihua Ran, Hui Li, Jianfeng Fu, Ling Liu, Yanchao Xing, Xiumei Li, Hongming Shen, Yan Chen, Xiaofang Jiang, Yan Li, Huiwu Li
2013 BMC Systems Biology  
analysis of the Protein-protein interaction (PPI) network.  ...  Essential hypertension (EH) is a complex disease as a consequence of interaction between environmental factors and genetic background, but the pathogenesis of EH remains elusive.  ...  The newest version of STRING, 9.0, covers approximately 2.5 million proteins from 630 different organisms [9] .  ... 
doi:10.1186/1752-0509-7-32 pmid:23587307 pmcid:PMC3641020 fatcat:jcyoqel7a5akzfqaqxbtajjupm

Protein Interaction Networks: Protein Domain Interaction and Protein Function Prediction [chapter]

Yanjun Qi, William Stafford Noble
2011 Handbook of Statistical Bioinformatics  
Most of a cell's functional processes involve interactions among proteins, and a key challenge in proteomics is to better understand these complex interaction graphs at a systems level.  ...  Because of their importance in development and disease, protein-protein interactions (PPIs) have been the subject of intense research in recent years.  ...  The most recent version of STRING [41] covers about 2.5 million proteins from 630 organisms. The authors claim that this provides the most comprehensive view of PPIs currently available.  ... 
doi:10.1007/978-3-642-16345-6_21 fatcat:whl2kgd3rbfcjm3ljkd56tj7vq

Global Proteomics Revealed Klebsiella pneumoniae Induced Autophagy and Oxidative Stress in Caenorhabditis elegans by Inhibiting PI3K/AKT/mTOR Pathway during Infection

Arumugam Kamaladevi, Krishnaswamy Balamurugan
2017 Frontiers in Cellular and Infection Microbiology  
FIGURE 2 | 2 Protein-protein interaction of the proteins identified at (A) 12 h, (B) 24 h, and (C) 36 h using STRING 10.0 software and based on their function the identified proteins were classified using  ...  based on their functions.  ...  The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with  ... 
doi:10.3389/fcimb.2017.00393 pmid:28932706 pmcid:PMC5592217 fatcat:27tbtp375rcapn5ywe2csllr5e

A Systems Biology Approach for the Investigation of the Heparin/Heparan Sulfate Interactome

Alessandro Ori, Mark C. Wilkinson, David G. Fernig
2011 Journal of Biological Chemistry  
A global view on how protein-HS interactions influence the extracellular proteome and, consequently, cell function is currently lacking.  ...  Here, we systematically investigate the functional and structural properties that characterize HS-interacting proteins and the network they form.  ...  A global view on how protein-HS interactions influence the extracellular proteome and, consequently, cell function is currently lacking.  ... 
doi:10.1074/jbc.m111.228114 pmid:21454685 pmcid:PMC3103365 fatcat:rrm4majavncyjdui5lyq42xbra

An optimized TOPS+ comparison method for enhanced TOPS models

Mallika Veeramalai, David Gilbert, Gabriel Valiente
2010 BMC Bioinformatics  
Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological  ...  Results: We have developed a TOPS+ string model as an improvement to the TOPS [1-3] graph model by considering loops as secondary structure elements (SSEs) in addition to helices and strands, representing  ...  Acknowledgements We would like to thank the TOPS Project for TOPS data resources and Juris Viksna for advice on our method. MV has been supported by a PhD studentship from the University of Glasgow.  ... 
doi:10.1186/1471-2105-11-138 pmid:20236520 pmcid:PMC2858036 fatcat:g43vpv4ntzat5cb6uulw4qjgci
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