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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 T Doncheva, John H Morris, Peer Bork, Lars J Jensen, Christian von Mering
2018 Nucleic Acids Research  
The most important new feature is 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  ...  The STRING database aims to collect, score and integrate all publicly available sources of protein-protein interaction information, and to complement these with computational predictions.  ...  Yuan for excellent IT support at EMBL. Thomas Rattei and his SIMAP project at University of Vienna provided essential protein similarity data for our very large sequence space.  ... 
doi:10.1093/nar/gky1131 pmid:30476243 fatcat:l6c2fugi3re7pk7agroo52cqqq

POS0848 IDENTIFICATION OF POTENTIAL CRUCIAL GENES AND KEY PATHWAYS IN PULMONARY ARTERIAL HYPERTENSION WITH SYSTEMIC SCLEROSIS BY BIOINFORMATIC ANALYSIS

S. Feng, S. X. Zhang, R. Zhao, C. Zheng, L. Cheng, T. Kong, X. Sun, Q. Wang, X. Li, Q. Yu, P. F. He
2021 Annals of the Rheumatic Diseases  
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.  ...  Finally, after the selected differential genes were introduced into STRING online software, the data information of protein interaction network was derived, and 12 core genes in the network were identified  ...  STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.  ... 
doi:10.1136/annrheumdis-2021-eular.1947 fatcat:ya2wzko7mra4noet2z6ehyva7q

BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley, Hordeum vulgare L

Sungho Lee, Tak Lee, Sunmo Yang, Insuk Lee
2020 Frontiers in Plant Science  
However, the functional annotation of its genome is relatively poor compared with other major crops.  ...  We have thus developed BarleyNet, a co-functional network of 26,145 barley genes, along with a web server for network-based predictions (http://www.inetbio.org/barleynet).  ...  STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.  ... 
doi:10.3389/fpls.2020.00098 pmid:32133024 pmcid:PMC7040090 fatcat:7laysai2sjgdzpukrlkuctdici

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 v11: protein-protein association networks with in- 10.1016/j.ijrobp.2003.11.041 creased coverage, supporting functional discovery in ge- 17. Milligan G, Kostenis E.  ...  Heterotrimeric G-proteins: a short nome-wide experimental datasets. Nucleic Acids Res. 2019;47: history. Br J Pharmacol. 2006;147:S46-55. https://doi.org/10.  ... 
doi:10.15324/kjcls.2021.53.4.353 fatcat:t5gb2n66n5h2pesb2avtcuxhei

The Role of Interleukin-4 VNTR Polymorphism in Dysmenorrhea Development

Mehmet Esen, Ayşe Feyda Nursal, Esra Duman, Serbülent Yiğit
2020 Haseki Tıp Bülteni  
Interleukin-4 (IL-4), a cytokine, regulates multiple biological functions.  ...  Results: The prevalence of genotypes of P1/P1, P1/P2, and P2/ P2 for IL-4 VNTR were 1.72%, 34.4%, and 63.7% in patients with PD, and 0.8%, 26.6%, and 72.5% in controls, respectively.  ...  IL-4 protein is evidenced with a square, STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.  ... 
doi:10.4274/haseki.galenos.2020.6162 fatcat:ttvxu5pwlba4lacdbyobmai7ku

A genome-wide CRISPR screen identifies regulators of beta cell function involved in type 2 diabetes risk [article]

Antje K Grotz, Elena Navarro-Guerrero, Romina J Bevacqua, Roberta Baronio, Soren K Thomsen, Sameena Nawaaz, Varsah Rajesh, Agata Wesolowska-Andersen, Seung K Kem, Daniel Ebner, Anna L Gloyn
2021 bioRxiv   pre-print
We identified 580 genes influencing this phenotype: integration with genetic and genomic data provided experimental support for 20 candidate type 2 diabetes effector transcripts including the autophagy  ...  Since many of the genetic signals for type 2 diabetes exert their effects through pancreatic islet-cell dysfunction, we performed a genome-wide pooled CRISPR loss-of-function screen in human pancreatic  ...  STRING v11: Protein-protein association networks with increased 627 coverage, supporting functional discovery in genome-wide experimental datasets.  ... 
doi:10.1101/2021.05.28.445984 fatcat:s2i7u3ooczem5mjxln5trevrh4

Identification of Potential Hub Genes and Therapeutic Drugs in Malignant Pleural Mesothelioma by Integrated Bioinformatics Analysis

Xiangxin Zhang, Liu Yang, Wei Chen, Ming Kong
2020 Oncology Research and Treatment  
The STRING database was used to construct a protein-protein interaction network, and modules analysis and hub genes acquisition were performed by Cytoscape.  ...  Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed by DAVID database.  ...  W.C. participated in analyzing the data and revising the manuscript. M.K. reviewed the manuscript. All authors reviewed the final manuscript.  ... 
doi:10.1159/000510534 pmid:33032291 fatcat:iqhh6j4nynenjj4hnbyociotly

Prediction of SARS-CoV interaction with host proteins during lung aging reveals a potential role for TRIB3 in COVID-19 [article]

Diogo de Moraes, Brunno Vivone Buquete Paiva, Sarah Santiloni Cury, Joao Pessoa Araujo, Marcelo Alves da Silva Mori, Robson Francisco Carvalho
2020 bioRxiv   pre-print
Functional enrichment analysis of age-related genes, in common with SARS-CoV-induced perturbations, revealed genes associated with the mitotic cell cycle and surfactant metabolism.  ...  with transcriptional changes in human protein-coding genes that potentially interact with these viruses.  ...  STRING v11: Protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47, D607-D613 (2019). 36.  ... 
doi:10.1101/2020.04.07.030767 fatcat:sd4az7ys35e4ja2dmg5vzq76se

Learning representations of molecules to predict intermolecular interactions by constructing a large-scale heterogeneous molecular association network

Hai-Cheng Yi, Zhu-Hong You, De-Shuang Huang, Zhen-Hao Guo, Keith C.C. Chan, Yangming Li
2020 iScience  
Molecular components that are functionally interdependent in human cells constitute molecular association networks. Disease can be caused by disturbance of multiple molecular interactions.  ...  To this end, a heterogeneous molecular association network is formed by systematically integrating comprehensive associations between miRNAs, lncRNAs, circRNAs, mRNAs, proteins, drugs, microbes, and complex  ...  STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.  ... 
doi:10.1016/j.isci.2020.101261 pmid:32580123 pmcid:PMC7317230 fatcat:4vpw2ykwyvdrjknq7w5zjuzyhq

Game theoretic centrality: a novel approach to prioritize disease candidate genes by combining biological networks with the Shapley value

Min Woo Sun, Stefano Moretti, Kelley M. Paskov, Nate T. Stockham, Maya Varma, Brianna S. Chrisman, Peter Y. Washington, Jae-Yoon Jung, Dennis P. Wall
2020 BMC Bioinformatics  
Complex human health conditions with etiological heterogeneity like Autism Spectrum Disorder (ASD) often pose a challenge for traditional genome-wide association study approaches in defining a clear genotype  ...  Top ranking genes with the highest game theoretic centrality in both the weighted and unweighted approaches were enriched for pathways previously associated with autism, including pathways of the immune  ...  Funding This work was supported in part by funds to DPW from the National Institute of Health (1R01EB025025-01 and 1R21HD091500-01), the Hartwell Foundation, Bill and Melinda Gates Foundation, Coulter  ... 
doi:10.1186/s12859-020-03693-1 pmid:32787845 fatcat:3a6vukek4jbcjpyby6kk3rk4by

Establishing gene regulatory networks from Parkinson's disease risk loci [article]

Sophie L Farrow, William Schierding, Sreemol Gokuladhas, Evgeniia Golovina, Tayaza M. Fadason, Antony A Cooper, Justin M. O'Sullivan
2021 bioRxiv   pre-print
The latest meta-analysis of genome wide association studies (GWAS) identified 90 independent single nucleotide polymorphisms (SNPs) across 78 genomic regions associated with Parkinson's disease (PD), yet  ...  To establish the functional gene regulatory networks associated with PD-SNPs, we utilised an approach combining spatial (chromosomal conformation capture) and functional (expression quantitative trait  ...  STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47, D607-D613 (2019). 37.  ... 
doi:10.1101/2021.04.08.439080 fatcat:4v3zir7myraonfrptemi4hthti

POS0849 SEXUAL FUNCTION IS IMPAIRED IN WOMEN WITH IDIOPATHIC INFLAMMATORY MYOPATHIES COMPARED TO HEALTHY CONTROLS

B. Heřmánková, M. Špiritović, S. Oreska, H. Štorkánová, H. Smucrova, M. Komarc, M. Klein, K. Pavelka, L. Šenolt, H. Mann, J. Vencovský, M. Tomčík
2021 Annals of the Rheumatic Diseases  
Worse scores in IIM were associated with disease-related features.Table 1.Sexual function and pelvic floor function in women with IIM and healthy controlsQuestionnaire: score range (meaning)IIM (n=62)HC  ...  These serious clinical manifestations can be associated with significant impairment of quality of life, including sexual life.Objectives:This study aimed to compare sexual function in patients with IIM  ...  Acknowledgements: This project was supported by National Science Foun-Acknowledgements: Supported by MHCR 023728, GA UK 1578119, and SVV  ... 
doi:10.1136/annrheumdis-2021-eular.1955 fatcat:4b4tymevb5eqbcvrc6dmtfnt64

Identification of serum prognostic marker miRNAs and construction of microRNA-mRNA networks of esophageal cancer

Yue Jiang, Chengda Zhang, Wenbin Shen, Yiming Li, Yun Wang, Jianjun Han, Tao Liu, Li Jia, Fei Gao, Xiaojun Liu, Mi Chen, Guangming Yi (+3 others)
2021 PLoS ONE  
The STRING database was used to obtain proteinprotein interaction (PPI) relationships to construct the DEM-DEG network.  ...  Furthermore, we selected core genes and core miRNAs associated with esophageal cancer prognosis by performing survival and univariate/multivariate COX analysis on DEMs and DEGs in the network and performed  ...  STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.  ... 
doi:10.1371/journal.pone.0255479 pmid:34329340 pmcid:PMC8323927 fatcat:btw7wb5jdrbu5a7ytvzdkunkq4

A Network Propagation Approach to Prioritize Long Tail Genes in Cancer [article]

Hussein Mohsen, Vignesh Gunasekharan, Tao Qing, Sahand Negahban, Zoltan Szallasi, Lajos Pusztai, Mark B. Gerstein
2021 bioRxiv   pre-print
We validate UMGs' role in cancer cell survival in vitro using genome-wide RNAi and CRISPR databases and report new cancer-pathway associations based on UMGs that were not previously identified using driver  ...  In this paper, we introduce a network propagation approach that focuses on long tail genes with potential functional impact on cancer development.ResultsWe identify sets of often overlooked, rarely to  ...  functional discovery in genome-wide experimental datasets.  ... 
doi:10.1101/2021.02.05.429983 fatcat:oum4y7g2wbfdvof3mbjfavlzfm

Gene co-expression analysis of human RNASEH2A reveals functional networks associated with DNA replication, DNA damage response, and cell cycle regulation [article]

Stefania Marsili, Ailone Tichon, Francesca Storici
2020 bioRxiv   pre-print
Additional examination of protein-protein networks for RNASEH2A by the STRING database analysis, revealed a high co-expression correlation between RNASEH2A and the genes of the protein networks identified  ...  Further bioinformatics investigation showed increased gene expression of RNASEH2A in different types of actively cycling cells and tissues, and particularly in several cancers, supporting a biological  ...  STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.  ... 
doi:10.1101/2020.08.27.270595 fatcat:zwzootctlncl7iru4a2q6s6jl4
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