Data of the interacting protein networks and nucleotide metabolism pathways related to NDK and NT5

Zhang, Dan; Ma, Wen; He, Yu; He, Gu; Zhang, Peng; Zhu, Hongxia; Xu, Nuo; Liang, Shufang

doi:10.1016/j.dib.2016.11.029

Cited by 5 publications

(3 citation statements)

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“…We analyzed the interaction between lncRNA and protein using the STRING online software [13] and the combined score > 0.4 was used as the cutoff criterion [14]. The PPI network was built using Cytoscape software [15].…”

Section: Identification Of Lncrna-associated Ppi Modulesmentioning

confidence: 99%

Construction of relapse-related lncRNA-mediated ceRNA networks in Hodgkin lymphoma

Liang

Zhu

Chen

et al. 2020

aoms

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Introduction: Hodgkin lymphoma (HL) is a type of lymphoma common throughout the western countries. However, the detailed mechanisms and special biomarkers of HL remain to be further investigated. Emerging studies have shown that long non-coding RNAs play a key role in human cancers. Material and methods: In the present work, we constructed relapse-related lncRNA-mediated ceRNA networks in HL. Additionally, we constructed co-expression networks for these relapse-related lncRNAs. We also constructed a relapse-related lncRNA-miRNA-mRNA network to study the potential mechanism of these lncRNAs. Furthermore, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to explore functions of DEGs in Hodgkin lymphoma. Results: A total of 18 lncRNAs were found to be dysregulated between early relapse and late relapse HL. Six lncRNAs (PCBP1-AS1, HCG18, GAS5, PSMD6-AS2, PRKCQ-AS1, SNHG6), 116 mRNAs and 121 miRNAs were included in the ceRNA network. Bioinformatics analyses revealed that these lncRNAs were significantly involved in regulating immune system processes, responses to chemical stimuli and responses to stress. Among them, HCG18 and PCBP1-AS1 were identified as key lncRNAs in HL relapse. Conclusions: Our results for the first time constructed the key relapse-related lncRNA-mediated ceRNA networks in Hodgkin lymphoma progression. We trust that this work will provide a new therapeutic and prognostic target for HL.

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Section: Identification Of Lncrna-associated Ppi Modulesmentioning

confidence: 99%

Construction of relapse-related lncRNA-mediated ceRNA networks in Hodgkin lymphoma

Liang

Zhu

Chen

et al. 2020

aoms

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“…The gene adk , and py are essential in nt 5-mediated nucleic acid metabolism of S. aureus based on the reported literature and bioinformatics analysis by STRING software (http://string-db.org/cgi/input.pl) (19). We further verified if nt 5 gene mutation had influences on the two gene transcription levels.…”

Section: Resultsmentioning

confidence: 99%

Staphylococcus aureus nt5 gene contributes to bacterial infection ability to form kidney abscess

Yang¹,

Liu²,

Xia

et al. 2022

Preprint

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Staphylococcus aureus (S. aureus) is a commonly conditional infection pathogen, in which several key virulence genes are responsible for bacterial infection ability. The S. aureus nt5 gene, encoding 5’-nucleotidase, mediates bacterial nucleic acid pathway, yet it is nearly unknown of nt5 function for staphylococcal infection ability. Herein we have constructed S. aureus mutant with the gene nt5C166T silence (S. aureus Δnt5) by a CRISPR RNA-guided base editing system to investigate bacterial infection ability in vitro and in vivo. As expected, several nt5-related genes are disturbed in S. aureus Δnt5, in which gene transcription level of py is decreased compared with the wild-type S. aureus. Bacterial gene nt5 is downregulated and py/adk are upregulated when S. aureus is exposed to antibiotics daptomycin, which indicates nt5-mediated nucleic acid pathway is interfered upon with daptomycin treatment. Furthermore, the mutant Δnt5 displays about a 40-fold reduction of bacterial loading in mouse kidney on a mouse sepsis model, and the infection ability of Δnt5 is reduced than the wild-type bacteria. The gene nt5 contributes to S. aureus-infected abscess formation in mouse kidney, and the silence of nt5 gene promotes phagocytosis of S. aureus by mouse and human immunocytes. In general, our findings reveal nt5 silence impedes bacterial loading in kidney to form abscess but enhances S. aureus to be phagocytosed by host cell immune system in vitro and in vivo, which indicates that nt5 gene plays an important role in bacterial infection and immune evasion.

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“…We applied the analysis of the interaction between lncRNA and protein by utilizing STRING online software was utilized to analyze (Zhang et al, 2016) and the combined score >0.4 was used as the cut-off criterion (Yan et al, 2017). The PPI network was built by utilizing Cytoscape software (Kohl et al, 2011).…”

Section: Methodsmentioning

confidence: 99%

Identification of Key lncRNAs Associated With Atherosclerosis Progression Based on Public Datasets

et al. 2019

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Atherosclerosis is one of the most common type of cardiovascular disease and the prime cause of mortality in the aging population worldwide. However, the detail mechanisms and special biomarkers of atherosclerosis remain to be further investigated. Lately, long non-coding RNAs (lncRNAs) has attracted much more attention than other types of ncRNAs. In our work, we found and confirmed differently expressed lncRNAs and mRNAs in atherosclerosis by analyzing GSE28829. We performed the weighted gene co-expression network analysis (WGCNA) by analyzing GSE40231 to confirm highly correlated genes. Gene Ontology (GO) analysis were utilized to assess the potential functions of differential expressed lncRNAs in atherosclerosis. Co-expression networks were also constructed to confirm hub lncRNAs in atherosclerosis. A total of 5784 mRNAs and 654 lncRNAs were found to be dysregulated in the progression of atherosclerosis. A total of 15 lncRNA-mRNA co-expression modules were identified in this study based on WGCNA analysis. Moreover, a few lncRNAs, such as ZFAS1, LOC100506730, LOC100506691, DOCK9-AS2, RP11-6I2.3, LOC100130219, were confirmed as important lncRNAs in atherosclerosis. Taken together, bioinformatics analysis revealed these lncRNAs were involved in regulating the leukotriene biosynthetic process, gene expression, actin filament organization, t-circle formation, antigen processing, and presentation, interferon-gamma-mediated signaling pathway, and activation of GTPase activity. We believed that this study would provide potential novel therapeutic and prognostic targets for atherosclerosis.

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Data of the interacting protein networks and nucleotide metabolism pathways related to NDK and NT5

Cited by 5 publications

References 1 publication

Construction of relapse-related lncRNA-mediated ceRNA networks in Hodgkin lymphoma

Construction of relapse-related lncRNA-mediated ceRNA networks in Hodgkin lymphoma

Staphylococcus aureus nt5 gene contributes to bacterial infection ability to form kidney abscess

Identification of Key lncRNAs Associated With Atherosclerosis Progression Based on Public Datasets

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