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Mining Functional Gene Modules Linked with Rheumatoid Arthritis Using a SNP-SNP Network

Genomics, Proteomics & Bioinformatics 2012年第1期10卷 23-34页

作者： Lin Hua Hui Lin Dongguo Li Lin Li Zhicheng Liu Biomedical Engineering Institute Capital Medical UniversityBeijing 100069China

The identification of functional gene modules that are derived from integration of information from different types of networks is a powerful strategy for interpreting the etiology of complex diseases such as rheumatoid arthritis （RA）. Genetic variants are known to increase the risk of developing RA. Here, a novel method, the construction of a genetic network, was used to mine functional gene modules linked with RA. A polymorphism interaction analy- sis （PIA） algorithm was used to obtain cooperating single nucleotide polymorphisms （SNPs） that contribute to RA disease. The acquired SNP pairs were used to construct a SNP-SNP network. Sub-networks defined by hub SNPs were then extracted and turned into gene modules by mapping SNPs to genes using dbSNP database. We per- formed Gene Ontology （go） analysis on each gene module, and some go terms enriched in the gene modules can be used to investigate clustered gene function for better understanding RA pathogenesis. This method was applied to the Genetic analysis Workshop 15 （GAW 15） RA dataset. The results show that genes involved in func- tional gene modules, such as CD160 （rs744877） and RUNX1 （rs2051179）, are especially relevant to RA, which is supported by previous reports. Furthermore, the 43 SNPs involved in the identified gene modules were found to be the best classifiers when used as variables for sample classification.

关键词： polymorphism interaction analysis hub SNP sub-networks go enrichment analysis

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Mechanism of Wumei Pill in the Treatment of Non-Erosive reflux disease from the Perspective of Network Pharmacology and Molecular docking

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Asian Toxicology Research 2021年第4期3卷 1-13页

作者： Yihua Fan Tengda Li Rui gong Wen Zhang Fenghua Yu Xinju Li Department of Rheumatism and Immunity First Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjin300193China National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion Tianjin 300381China College of Traditional Chinese Medicine Tianjin University of Traditional Chinese MedicineTianjin301617China College of Pharmaceutical Engineering of Traditional Chinese Medicine Tianjin University of Traditional Chinese MedicineTianjin301617China

Objective:Based on network pharmacology and molecular docking to explore the mechanism of Wumei Pill in the treatment of non-erosive reflux disease(NERD).Method:We collected the active ingredients and targets of Wumei Pill by Traditional Chinese Medicine Systems Pharmacology Database and analysis Platform(TCMSP),and collected NERD related targets through Genecards,PharmGKB,Drugbank,DisGeNET,OMIM,CTD and TTD *** targets of Wumei Pill targets and NERD related targets were the potential targets of Wumei Pill in the treatment of *** imported the intersection targets into the STRING database to obtain the PPI network,and obtained the hub *** network diagram of"Drugs-Potential active ingredients-Potential targets"was constructed by Cytoscape 3.7.2 *** used R software to perform Gene Ontology function enrichment analysis(go)and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis(KEGG)on hub targets,and then performed molecular docking ***:There were 129 active ingredients and 213 drug targets of Wumei Pill of which 114 were the intersection targets.1587 go enrichment items were identified(P<0.05),including 1,491 biological processes,11 cell components,and 85 molecular functions.143 KEGG pathways(P<0.05),mainly related to Kaposi sarcoma-associated herpesvirus infection,IL-17 signaling pathway,the TNF signaling pathway,MAPK signaling *** of molecular docking showed that the potential active ingredients in Wumei Pill had relatively stable binding activity to the key ***:Wumei pill for the treatment of non-erosive reflux disease are main active ingredients quercetin,kaempferol,beta sitosterol,Isocorypalmine,Stigmasterol,rutaecarpine,etc,the main targets is JUN,TP53,AKT1,may inhibit excessive inflammation,antioxidant therapy effect into full *** provided a certain theoretical basis for clinical application.

关键词： Network Pharmacology Wumei Pill Non erosive acid reflux disease go enrichment analysis KEGG Pathway analysis Molecular docking

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