scholarly journals Systematic analysis of molecular mechanisms for HCC metastasis via text mining approach

Oncotarget ◽  
2017 ◽  
Vol 8 (8) ◽  
pp. 13909-13916 ◽  
Author(s):  
Cheng Zhen ◽  
Caizhong Zhu ◽  
Haoyang Chen ◽  
Yiru Xiong ◽  
Junyuan Tan ◽  
...  
Keyword(s):  
Text Mining ◽  
Molecular Mechanisms ◽  
Systematic Analysis

scholarly journals Systematic Analysis of Endometrial Cancer-Associated Hub Proteins Based on Text Mining

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Huiqiao Gao ◽  
Zhenyu Zhang
Keyword(s):  
Endometrial Cancer ◽  
Targeted Therapy ◽  
Text Mining ◽  
Molecular Mechanisms ◽  
Ppi Network ◽  
Systematic Analysis ◽  
Ppi Networks ◽  
Related Proteins ◽  
Gene Data ◽  
Hub Proteins

Objective. The aim of this study was to systematically characterize the expression of endometrial cancer- (EC-) associated genes and to analysis the functions, pathways, and networks of EC-associated hub proteins.Methods. Gene data for EC were extracted from the PubMed (MEDLINE) database using text mining based on NLP. PPI networks and pathways were integrated and obtained from the KEGG and other databases. Proteins that interacted with at least 10 other proteins were identified as the hub proteins of the EC-related genes network.Results. A total of 489 genes were identified as EC-related withP<0.05, and 32 pathways were identified as significant (P<0.05,FDR<0.05). A network of EC-related proteins that included 271 interactions was constructed. The 17 proteins that interact with 10 or more other proteins (P<0.05,FDR<0.05) were identified as the hub proteins of this PPI network of EC-related genes. These 17 proteins are EGFR, MET, PDGFRB, CCND1, JUN, FGFR2, MYC, PIK3CA, PIK3R1, PIK3R2, KRAS, MAPK3, CTNNB1, RELA, JAK2, AKT1, and AKT2.Conclusion. Our data may help to reveal the molecular mechanisms of EC development and provide implications for targeted therapy for EC. However, corrections between certain proteins and EC continue to require additional exploration.

scholarly journals A Systematic Analysis of Candidate Genes Associated with Nicotine Addiction

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Meng Liu ◽  
Xia Li ◽  
Rui Fan ◽  
Xinhua Liu ◽  
Ju Wang
Keyword(s):  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Nicotine Addiction ◽  
Clustering Coefficient ◽  
Functional Enrichment ◽  
Moderate Degree ◽  
Cancer Genes ◽  
Systematic Analysis ◽  
The Central Nervous System

Nicotine, as the major psychoactive component of tobacco, has broad physiological effects within the central nervous system, but our understanding of the molecular mechanism underlying its neuronal effects remains incomplete. In this study, we performed a systematic analysis on a set of nicotine addiction-related genes to explore their characteristics at network levels. We found that NAGenes tended to have a more moderate degree and weaker clustering coefficient and to be less central in the network compared to alcohol addiction-related genes or cancer genes. Further, clustering of these genes resulted in six clusters with themes in synaptic transmission, signal transduction, metabolic process, and apoptosis, which provided an intuitional view on the major molecular functions of the genes. Moreover, functional enrichment analysis revealed that neurodevelopment, neurotransmission activity, and metabolism related biological processes were involved in nicotine addiction. In summary, by analyzing the overall characteristics of the nicotine addiction related genes, this study provided valuable information for understanding the molecular mechanisms underlying nicotine addiction.

scholarly journals Identification of biological pathways and genes associated with neurogenic heterotopic ossification by text mining

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8276 ◽  
Author(s):  
Yichong Zhang ◽  
Yuanbo Zhan ◽  
Yuhui Kou ◽  
Xiaofeng Yin ◽  
Yanhua Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Text Mining ◽  
Heterotopic Ossification ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Egf Receptor ◽  
Enrichment Analysis ◽  
Biological Pathways ◽  
Specific Gene ◽  
Cord Injury

Background Neurogenic heterotopic ossification is a disorder of aberrant bone formation affecting one in five patients sustaining a spinal cord injury or traumatic brain injury (SCI-TBI-HO). However, the underlying mechanisms of SCI-TBI-HO have proven difficult to elucidate. The aim of the present study is to identify the most promising candidate genes and biological pathways for SCI-TBI-HO. Methods In this study, we used text mining to generate potential explanations for SCI-TBI-HO. Moreover, we employed several additional datasets, including gene expression profile data, drug data and tissue-specific gene expression data, to explore promising genes that associated with SCI-TBI-HO. Results We identified four SCI-TBI-HO-associated genes, including GDF15, LDLR, CCL2, and CLU. Finally, using enrichment analysis, we identified several pathways, including integrin signaling, insulin pathway, internalization of ErbB1, urokinase-type plasminogen activator and uPAR-mediated signaling, PDGFR-beta signaling pathway, EGF receptor (ErbB1) signaling pathway, and class I PI3K signaling events, which may be associated with SCI-TBI-HO. Conclusions These results enhance our understanding of the molecular mechanisms of SCI-TBI-HO and offer new leads for researchers and innovative therapeutic strategies.

scholarly journals Advancing Drug Discovery and Development from Active Constituents of Yinchenhao Tang, a Famous Traditional Chinese Medicine Formula

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Aihua Zhang ◽  
Hui Sun ◽  
Shi Qiu ◽  
Xijun Wang
Keyword(s):  
Systems Biology ◽  
Drug Discovery ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Molecular Mechanisms ◽  
Synergistic Effects ◽  
Molecular Networks ◽  
Agile Development ◽  
Therapeutic Effects ◽  
Systematic Analysis

Traditional Chinese medicine (TCM) formula has been playing a very important role in health protection and disease control for thousands of years. Guided by TCM syndrome theories, formula are designed to contain a combination of various kinds of crude drugs that, when combined, will achieve synergistic efficacy. However, the precise mechanism of synergistic action remains poorly understood. One example is a famous TCM formula Yinchenhao Tang (YCHT), whose efficacy in treating hepatic injury (HI) and Jaundice syndrome, has recently been well established as a case study. We also conducted a systematic analysis of synergistic effects of the principal compound using biochemistry, pharmacokinetics and systems biology, to explore the key molecular mechanisms. We had found that the three component (6,7-dimethylesculetin (D), geniposide (G), and rhein (R)) combination exerts a more robust synergistic effect than any one or two of the three individual compounds by hitting multiple targets. They can regulate molecular networks through activating both intrinsic and extrinsic pathways to synergistically cause intensified therapeutic effects. This paper provides an overview of the recent and potential developments of chemical fingerprinting coupled with systems biology advancing drug discovery towards more agile development of targeted combination therapies for the YCHT.

scholarly journals Chemical safety in the context of environmental goals of sustainable development

2021 ◽  
Vol 915 (1) ◽  
pp. 012032
Author(s):  
A Ishchenko ◽  
N Stuchynska ◽  
L Haiova ◽  
E Shchepanskiy
Keyword(s):  
Sustainable Development ◽  
Molecular Mechanisms ◽  
Hazardous Chemicals ◽  
Chemical Labeling ◽  
Chemical Safety ◽  
Systematic Analysis ◽  
Environmental Aspect ◽  
Treatment And Prevention ◽  
Chemical Products ◽  
Environmental Goals

Abstract The aim of the article is to carry out a systematic analysis of the components of chemical safety in the context of the environmental aspect of sustainable development goals and to identify those components with the help of competent health professionals. Hazardous chemicals can travel for long distances, be accumulated in the environment as well as cause adverse effects on human health through food chains. The action of toxicants of inorganic and organic nature occurs due to the violation of metabolic processes, inhibition of enzymes, and biotransformation of xenobiotics into more toxic compounds. Physicians must be clearly aware of the relationship in the “toxicant-pathology” system; understand the molecular mechanisms of the hazardous chemicals action; use terminology regarding toxicological characteristics of toxicants; conduct educational, treatment, and prevention activities among the population; acquire information on regulations governing the management of chemical compounds. The next component of chemical safety is the knowledge of approaches to chemical labeling and safety measures for working with chemical products throughout their life cycle. Proper interpretation of the type and level of hazard will enable taking necessary precautions and following relevant safety rules while working with chemical products.

scholarly journals Network Pharmacology-Based Systematic Analysis of Molecular Mechanisms of Geranium wilfordii Maxim for HSV-2 Infection

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Hao Zhang ◽  
Ming-Huang Gao ◽  
Yang Chen ◽  
Tao Liu
Keyword(s):  
Molecular Docking ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Pharmacological Study ◽  
Network Pharmacology ◽  
System Response ◽  
Cytokine Signaling ◽  
Bioactive Substances ◽  
Systematic Analysis ◽  
Specific Distribution

Background. Being a traditional Chinese medicine, Geranium wilfordii Maxim (GWM) is used for the treatment of various infectious diseases, and its main active ingredients are the polyphenolic substances such as polyphenols quercetin, corilagin, and geraniin. Previous studies have demonstrated the anti-HSV-1 viral activity of these three main ingredients. Through employing a network pharmacological method, the authors of the present research intend to probe the mechanism of GWM for the therapeutic treatment of HSV-2 infection. Methods. The bioactive substances and related targets of GWM were obtained from the TCMSP database. Gene expression discrepancy for HSV-2 infection was obtained from dataset GSE18527. Crossover genes between disease target genes and GWM target genes were gained via Circos package. Distinctively displayed genes (DDGs) during HSV-2 infection were uploaded to the Metascape database with GWM target genes for further analysis. The tissue-specific distribution of the genes was obtained by uploading the genes to the PaGenBase database. Ingredient-gene-pathway (IGP) networks were constructed using Cytoscape software. Molecular docking investigations were carried out utilizing AutoDock Vina software. Results. Nine actively involved components were retrieved from the TCMSP database. After taking the intersection among 153 drug target genes and 83 DDGs, 7 crossover genes were screened. Gene enrichment analysis showed that GWM treatment of HSV-2 infection mainly involves cytokine signaling in the immune system, response to virus, epithelial cell differentiation, and type II interferon signaling (IFNG). One hub, three core objectives, and two critical paths were filtered out from the built network. Geraniin showed strong binding activity with HSV-2 gD protein and STING protein in molecular docking. Conclusions. This network pharmacological study provides a fundamental molecular mechanistic exploration of GWM for the treatment of HSV-2 infection.

scholarly journals Network Pharmacology-Based Systematic Analysis of Molecular Mechanisms of Dingji Fumai Decoction for Ventricular Arrhythmia

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Yi Liang ◽  
Bo Liang ◽  
Xin-Rui Wu ◽  
Wen Chen ◽  
Li-Zhi Zhao
Keyword(s):  
Molecular Docking ◽  
Ventricular Arrhythmia ◽  
Molecular Mechanisms ◽  
Mendelian Inheritance ◽  
Network Pharmacology ◽  
Ppi Network ◽  
Systematic Analysis ◽  
Chemical Structures ◽  
Function Modules ◽  
Underlying Mechanisms

Background. Dingji Fumai Decoction (DFD), a traditional herbal mixture, has been widely used to ventricular arrhythmia (VA) in clinical practice in China. However, research on the bioactive components and underlying mechanisms of DFD in VA is still scarce. Methods. Components of DFD were collected from TCMSP, ETCM, and literature. The chemical structures of each component were obtained from PubChem. Next, SwissADME and SwissTargetPrediction were applied for compounds screening and targets prediction of DFD; meanwhile, targets of VA were collected from DrugBank and Online Mendelian Inheritance in Man (OMIM). Then, the H-C-T-D network and the protein-protein interaction (PPI) network were constructed based on the data obtained above. CytoNCA was utilized to filter hub genes and VarElect was used to analyze the relationship between genes and diseases. At last, Metascape was employed for systematic analysis on the potential targets of herbals against VA, and AutoDock was applied for molecular docking to verify the results. Results. A total of 434 components were collected, 168 of which were qualified, and there were 28 shared targets between DFD and VA. Three function modules of DFD were found from the PPI network. Further systematic analysis of shared genes and function modules explained the potential mechanism of DFD in the treatment of VA; molecular docking has verified the interactions. Conclusions. DFD could be employed for VA through mechanisms, including complex interactions between related components and targets, as predicted by network pharmacology and molecular docking. This work confirmed that DFD could apply to the treatment of VA and promoted the explanation of DFD for VA in the molecular mechanisms.

scholarly journals Systematic analysis of breast atypical hyperplasia-associated hub genes and pathways based on text mining

2019 ◽  
Vol 28 (6) ◽  
pp. 507-514 ◽  
Author(s):  
Wei Ma ◽  
Bei Shi ◽  
Fangkun Zhao ◽  
Yunfei Wu ◽  
Feng Jin
Keyword(s):  
Text Mining ◽  
Atypical Hyperplasia ◽  
Hub Genes ◽  
Systematic Analysis

scholarly journals Is the Membrane Lipid Matrix a Key Target for Action of Pharmacologically Active Plant Saponins?

2021 ◽  
Vol 22 (6) ◽  
pp. 3167
Author(s):  
Svetlana S. Efimova ◽  
Olga S. Ostroumova
Keyword(s):  
Lipid Bilayers ◽  
Molecular Mechanisms ◽  
Antimicrobial Agents ◽  
Positive Curvature ◽  
Lipid Vesicles ◽  
Membrane Lipid ◽  
Systematic Analysis ◽  
Boundary Potential ◽  
Model Lipid Membranes ◽  
Pharmacologically Active

This study was focused on the molecular mechanisms of action of saponins and related compounds (sapogenins and alkaloids) on model lipid membranes. Steroids and triterpenes were tested. A systematic analysis of the effects of these chemicals on the physicochemical properties of the lipid bilayers and on the formation and functionality of the reconstituted ion channels induced by antimicrobial agents was performed. It was found that digitonin, tribulosin, and dioscin substantially reduced the boundary potential of the phosphatidylcholine membranes. We concluded that saponins might affect the membrane boundary potential by restructuring the membrane hydration layer. Moreover, an increase in the conductance and lifetime of gramicidin A channels in the presence of tribulosin was due to an alteration in the membrane dipole potential. Differential scanning microcalorimetry data indicated the key role of the sapogenin core structure (steroid or triterpenic) in affecting lipid melting and disordering. We showed that an alteration in pore forming activity of syringomycin E by dioscin might be due to amendments in the lipid packing. We also found that the ability of saponins to disengage the fluorescent marker calcein from lipid vesicles might be also determined by their ability to induce a positive curvature stress.

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