For a better understanding of the regulatory role of miRNAs in coordinating gene expression, we here present a systems biology ... We first construct a p21 regulatory network based on data from the literature and further expand it using algorithms that ... Based on the network structure, a detailed mechanistic model is established and its parameter values are determined using data ... Such an approach is characterized by an iterative process, including biological data acquisition and integration, network ...

Finally, we used Cytoscape (3.9.1) to extensively examine the gene regulatory network related to cell fate. ,i,Results,/i,. ... we constructed the pseudotime trajectory of cell development and identified key regulatory genes using the Monocle R package ( ... Analysis of dynamic gene expression revealed that ,i,Gpx3,/i, was significantly upregulated during cell differentiation into ... was predicted to be involved in the regulation of genes related to antioxidant stress and angiogenesis, suggesting a role in ...

Network and pathway analyses revealed functionally related genes interacting in gene regulatory networks and multiple ... We performed network and pathway analyses to discover molecular networks and signalling pathways enriched for germline and ... i,Results,/i,. The investigation revealed signatures of differentially expressed and differentially somatic mutated genes ... integrative genomics is a powerful approach for delineating oncogenic interactions between genes containing germline and genes ...

M. Štros, "HMGB proteins: interactions with DNA and chromatin," Biochimica et Biophysica Acta-Gene Regulatory Mechanisms, vol. ... R. Sgarra, S. Zammitti, A. Lo Sardo et al., "HMGA molecular network: from transcriptional regulation to chromatin remodeling," ... Different isoforms of the human protein HMGB1, encoded by the HMGB1 gene, have been reported [17] and other genes (HMGB2 and ... Biochimica et Biophysica Acta-Gene Regulatory Mechanisms, vol. 1799, no. 1-2, pp. 119-130, 2010. ...

The results of the miRNA-prognostic DEPRG-TF regulatory network showed that GSDMC, IRF1, and PLCG1 were regulated by both ... A miRNA-prognostic DEPRG-transcription factor (TF) regulatory network was created via the miRNet online tool. A risk score ... However, the efficacy of using pyroptosis-related genes (PRGs) in predicting the prognosis of pancreatic adenocarcinoma (PAAD) ... and gene set variation analysis (GSVA) was performed. Finally, the efficacy of certain potential drugs was predicted using the ...

... and regulate various biological processes via interactions with other genes thus forming a variety of complex networks. ... Therefore, it is critical to understand the relationship (e.g., interactions) between genes across different types of cancer in ... In a biological system, genes perform different molecular functions ... method using three key pathways related to cancer and demonstrate that it is capable of finding meaningful alterations in gene ...

Analysis from the Gene Expression Omnibus datasets supported the mRNA findings. High nuclear immunohistochemical NRF1 ... "Construction of disease-specific transcriptional regulatory networks identifies co-activation of four gene in esophageal ... It is a main inductor of genes of antioxidant proteins and phase II detoxifying enzymes [1]. In addition, due to activating ... K. J. Livak and T. D. Schmittgen, "Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta ...

Additionally, protein-protein interaction network analysis identified 10 hub genes, six (,i,FLT1,/i,, ,i,FLNB,/i,, ,i,FSTL3,/i ... The online search tool for the retrieval of interacting genes and Cytoscape software were used to identify hub genes, which ... We downloaded the GSE75010 and GSE10588 datasets from the GEO database and performed weighted gene coexpression network ... 17 genes were identified. KEGG and GO analyses further indicated the involvement of these genes in bioprocesses, such as ...

... networks. ,i,Methods,/i,. Firstly, normal and ccRCC PPI network were inferred and reweighted based on Pearson correlation ... Gene composition analyses of altered modules revealed that there were 56 common genes (such as ,i,MAPK1,/i,, ,i,CCNA2,/i,, and ... Finally, gene compositions of altered modules were analyzed, and pathways enrichment analyses of genes in altered modules were ... i,Conclusions,/i,. We successfully identified dysregulated genes and pathways of ccRCC in different stages, and these might be ...

... resulting in profound and complex regulatory networks [7]. In the cardiovascular system, miRNAs regulate basic functions in ... W. Wang, Y. Wang, W. Liu, and A. J. van Wijnen, "Regulation and biological roles of the multifaceted miRNA-23b (MIR23B)," Gene ... Furthermore, adenoviral-mediated gene transfer of miRNA-145/143, which downregulate the expression of this miRNAs after injury ... C. Catalanotto, C. Cogoni, and G. Zardo, "MicroRNA in control of gene expression: an overview of nuclear functions," ...

... autophagy and modulate the expression of immune-related factors by regulating the LKB1-mTOR-PI3KC signal transduction networks ... of proteins and genes related to the LKB1-mTOR-PI3KC signal transduction network in CD colon tissues to clarify the regulatory ... The calculation Ct (target gene) - Ct (internal reference gene) was used to obtain the △Ct value of each gene, the average △Ct ... Further observation of the role of the LKB1-mTOR-PI3KC signal transduction network in CD autophagy and the regulatory effect of ...

Noncoding RNA (ncRNA) is an important regulator involved in gene expression and can be detected in the cytoplasm or ... At present, the research on allergic rhinitis is more and more in-depth, and the regulatory network of lncRNA is gradually ... Further exploration of RNA in many ways will greatly expand the genes and molecules involved in the research on the mechanism ... Regulatory T cells (iTreg) and thymus-derived FOXP3+CD4+CD25+ natural regulatory T cells (nTreg) both play an important role in ...

... revealed that LAYN and its coexpressed genes primarily participated in immune response pathways, and LAYN expression was found ... J. Xu, J. Xu, X. Liu, and J. Jiang, "The role of lncRNA-mediated ceRNA regulatory networks in pancreatic cancer," Cell death ... As shown in Figure 4(d), 2 of the top 50 positively correlated genes are likely to be high-risk genes (. ), whereas eight of ... LAYN coexpressed genes and functional analyses in LIHC. (a) A scatter diagram of LAYN coexpressed genes. (b, c) The heatmaps of ...

However, the regulatory network was not well explored. This study was the first to highlight the role and molecular mechanism ... a database of regulatory networks between TFs and miRNAs sorted out from literature. GATA2 is a positive regulatory TF found in ... We further identified GPD1 as a direct target of miR-409-3p and GATA2 as an upstream regulatory gene of miR-409-3p. ... However, the regulatory network was not well explored. This study was the first to highlight the role and molecular mechanism ...

... and miRNA-mRNA-network investigations, were performed. The results of these analyses revealed that the differentially expressed ... which also provides the foundation for further research on the regulatory functions of exosomal miRNAs in the context of ADSC ... exosomal miRNAs participate in multiple biological processes, such as gene expression, synthesis of biomolecules, cell ... Additionally, bioinformatic analyses, which included gene ontology analyses, pathway analysis, ...

Compound-disease-target regulatory network analysis showed that AKT1, IL-6, TNF-,i,α,/i,, TP53, VEGFA, and APP were related to ... i,Results,/i,. This study obtained 1,009 IS disease gene sets. PPI network analysis identified 12 key targets: AGT, SAA1, KNG1 ... Database analyses retrieved 40 active ingredients and 47 target genes in SHD. The network proximity algorithm was used to ... network. Two methods were used to screen the key targets of IS disease based on the PPI network analysis. The TCMSP database ...

Quantitative real-time PCR for miR-34a and its targets; ,i,MET,/i, oncogene; gene-regulating apoptosis (,i,TP53INP2,/i, and ,i, ... Clinicopathological parameter correlation and in silico network analysis have also implicated. We found RCC tissues displayed ... These findings indicate miR-34a along with its putative target genes could play a role in RCC tumorigenesis and progression. ... This study aimed to evaluate the expression levels of miR-34a and 11 of its bioinformatically selected target genes and ...

These findings illustrated that ELAVL1 and APP were candidate crucial genes in the peripheral blood of CD patients. ELAVL1 ... Further taking all DEGs together, Gene Set Enrichment Analysis (GSEA) brought out the NOD-like receptor (NLR) signaling pathway ... NetworkAnalyst identified ELAV-like RNA binding protein 1 (ELAVL1) as the most crucial upregulated gene and amyloid-,i,β ... i, precursor protein (APP) as the most crucial downregulated gene in peripheral blood of CD patients. By computing significance ...

Therefore, unveiling the related novel molecular targets and networks participating in triggering and resisting the ... and/or silencing of its up-regulatory genes (e.g., FPR1 [127]) might be useful for preventing MIRI by suppressing cardiac ... supporting our understanding of the regulatory mechanisms of the protein interactions associated with the inflammatory network ... in the very dimension of gene expression. Accordingly, the overexpression of the upstream downregulatory genes of the MAPK ...

... and miR-634 upregulated the gene expression. These miRNAs which targeted ,i,β,/i,-catenin mRNA were confirmed by dual- ... These data suggested the existence of a regulatory network involving the circIFT80/miR-142, miR-634, miR-568/β-catenin pathways ... The expression levels of c-myc, the downstream target gene of β-catenin, changed in accordance with β-catenin (Figures 5(b) and ... Finally, the expression levels of these genes and miRNAs were calculated by the 2 −ΔΔCT method and presented as a bar chart. ...

R. C. Scarpulla, "Metabolic control of mitochondrial biogenesis through the PGC-1 family regulatory network," Biochimica et ... BECN1 gene deletion is often present in human breast, ovarian, and prostate cancers, and aging Becn1+/- mice are prone to ... C. Canto and J. Auwerx, "PGC-1α, SIRT1 and AMPK, an energy sensing network that controls energy expenditure," Current Opinion ... Gene that was identified as a tumor suppressor that is mutated in a large number of cancers at high frequency. ...

Western blotting was performed to detect the protein levels of TWIST and EMT-related genes. Luciferase reporter gene analysis ... The function and possible mechanism of lncRNA Small Nucleolar RNA Host Gene 3 (SNHG3) in GC have not been fully studied. The ... This will help us to better understand the lncRNA, miRNA, and mRNA network in GC. However, the function of lncRNA SNHG3, miR- ... According to the above experimental data, we speculated that the regulatory axis of lncRNA SNHG3-miR-326-TWIST might be related ...

In this study, the ,i,sp2,/i, gene was cloned and expressed in ,i,Escherichia coli,/i, to produce a 6xHis-tagged fusion protein ... The sp2 gene was inserted into the MCS of the transfer plasmid pFastBac-HTB between BamH I and Xho I sites and transformed into ... J. R. Vane, E. E. Anggard, and R. M. Botting, "Regulatory functions of the vascular endothelium," The New England Journal of ... Contribution to the pathophysiology of atherosclerosis?" European Cytokine Network, vol. 9, no. 4, pp. 697-698, 1998. ...

... gene mutation detection has become another important resource to investigate regulatory mechanisms and cellular processes. Some ... From this network, we found that, except for phosphorylation, the interactions among one kind of PTMs were less compared with ... X. Jiao, B. T. Sherman, D. W. Huang et al., "DAVID-WS: a stateful web service to facilitate gene/protein list analysis," ... L. Verdone, E. Agricola, M. Caserta, and E. di Mauro, "Histone acetylation in gene regulation," Briefings in Functional ...

Gene therapy through provision of a normal gene or stem cell transplantation has been attempted. Theoretically, X chromosome ... G. Calfa, J. J. Hablitz, and L. Pozzo-Miller, "Network hyperexcitability in hippocampal slices from MECP2 mutant mice revealed ... efforts in translational research and the necessary and critical collaboration with pharmaceutical enterprises and regulatory ... actually with more genes being activated than repressed [135]. The precise number and identification of genes affected are not ...

Through network analysis of the compound-target pathway, we identified hub molecular targets within these pathways including ... 3.3.1. Network Analysis. Active compound and target data extracted above were employed to construct a C-T-D network containing ... Gene Ontology and Pathway Analysis. Target enrichment gene ontology (GO) and pathway analyses lead us to gain mechanistic ... The regulatory roles of RORs and RXRs in the function of lymphoid cell have already been discussed previously [60, 61]. ...

R. I. Morimoto, "Proteotoxic stress and inducible chaperone networks in neurodegenerative disease and aging," Genes & ... Biochimica et Biophysica Acta-Gene Regulatory Mechanisms, vol. 1809, no. 2, pp. 80-87, 2011. ... F. Wang, S. Denison, J.-P. Lai et al., "Parkin gene alterations in hepatocellular carcinoma," Genes Chromosomes and Cancer, vol ... 3. A Close Network with UPS. 3.1. The UPS System. The proteasome is a large complicated protein machine of about 2.5 MDa. The ...

... induce the production of inflammatory mediators and cytokines in different immune cells and how histamine exerts regulatory ... Other mediators act as regulatory components to establish homeostasis after injury or prevent the inflammatory process. ... Lactobacillus reuteri is a member of the gut microbiota that belongs to the Firmicutes family; HDC gene expression by this ... Future studies may improve our understanding of the histamine network in organisms and its paradoxical nature. ...

i,Method,/i,. A multidimensional bioinformatics analysis was performed to examine the relationship between NRP genes and ... i,Conclusions,/i,. Neurovascular-related NRP family genes are significantly correlated with cancer prognosis, TME, and immune ... i,Background,/i,. Neurovascular-related genes have been implicated in the development of cancer. Studies have shown that a high ... Pan-cancer alterations of the MYC oncogene and its proximal network across The Cancer Genome Atlas," Cell Systems, vol. 6, no. ...

... and cytokeratin filament network (E-cadherin, occludins, type IV collagen, and laminin-1) [50, 52, 53]. Another feature of EMT ... Other regulatory molecular targets that can be exploited to retard tumor progression and metastasis are based on the fact that ... is the heterogeneity of the cell population which may be a product of varying degrees of gene alterations in the cell ...