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STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
2018
Nucleic Acids Research
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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
2021
Annals of the Rheumatic Diseases
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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
2020
Frontiers in Plant Science
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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
2021
Korean Journal of Clinical Laboratory Science
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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
2020
Haseki Tıp Bülteni
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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]
2021
bioRxiv
pre-print
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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
2020
Oncology Research and Treatment
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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]
2020
bioRxiv
pre-print
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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
2020
iScience
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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
2020
BMC Bioinformatics
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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]
2021
bioRxiv
pre-print
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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
2021
Annals of the Rheumatic Diseases
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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
2021
PLoS ONE
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The STRING database was used to obtain protein–protein 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]
2021
bioRxiv
pre-print
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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]
2020
bioRxiv
pre-print
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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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