Objective:To construct SET gene recombinant adenovirus vector and SET gene small interfering RNA(SiRNA) recombinant adenovirus vector for over-expression or knock-down of SET levels. Methods:The cDNA sequence of SET w...Objective:To construct SET gene recombinant adenovirus vector and SET gene small interfering RNA(SiRNA) recombinant adenovirus vector for over-expression or knock-down of SET levels. Methods:The cDNA sequence of SET was cloned by reverse transcriptive polymerase chain reaction(RT-PCR) and the SET gene fragment was subcloned into adenovirus shuttle plasmid pAdTrack-CMV to construct the shuttle plasmid pAdTrack-SET.The shuttle plasmid pAdtrack-SET was transformed into BJ5183 cells with the adenoviral backbone pAdEasy-1 to obtain the homologous recombinant Ad-CMV-SET and the recombinant Ad-CMV-SET was packaged and amplified in the AD293 cells.The expression of SET in AD293 cells was detected by Western blot.In addition,we constructed SET gene SiRNA recombinant adenovirus vector(Ad-H1-SiRNA/SET) and its efficacy of knockdown of SET protein was detected in infected GC-2spd(ts) cells by Western blot. Results:The recombinant adenovirus vectors,both SET gene recombinant adenovirus vector Ad-CMV-SET and SET gene SiRNA recombinant adenovirus vector Ad-H1-SiRNA/SET,were proven to be constructed successfully by the evidence of endonulease digestion and sequencing.AD293 cells infected with either recombinant adenovirus vector of Ad-CMV-SET or Ad-H1-SiRNA/SET were observed to express GFP.The expression of SET protein was up-regulated significantly in AD293 cells infected with SET gene recombinant adenovirus vector.On the contrast, SET protein was significantly down-regulated in the GC-2spd(ts) cells infected with Ad-H1-SiRNA/SET (P<0.05) and the knockdown efficiency was approximately 50%-70%. Conclusion:The recombinant adenovirus vector Ad-CMV-SET and Ad-H1-SiRNA/SET were successfully constructed and effectively expressed in germ cells and somatic cells.It provides an experimental tool for further study of SET gene in the physiological and pathophysiological mechanism of reproduction-related diseases.展开更多
Objective:To identify alpha-glucosidase inhibitors from Ficus benghalensis and analyze gene set enrichment of regulated protein molecules.Methods:The phytoconstituents of Ficu.s benghalen.sis were queried for inhibito...Objective:To identify alpha-glucosidase inhibitors from Ficus benghalensis and analyze gene set enrichment of regulated protein molecules.Methods:The phytoconstituents of Ficu.s benghalen.sis were queried for inhibitors of alphaglucosidase,also identified as aldose reductase inhibitors.Druglikeness score,absorption,distribution,metabolism,excretion and toxicity profile,biological spectrum,and gene expression were predicated for each compound.Docking study was performed to predict the binding affinity with alpha-glucosidase and aldose reductase and compared with clinically proven molecules.Kyoto Encyclopedia of Genes and Genomes pathway analysis was performed for the regulated genes to identify the modulated pathways.Results:Apigenin,3,4’,5,7-tetrahydroxy-3’-methoxyflavone,and kaempferol were identified as inhibitors of alpha-glucosidase and aldose reductase.Kaempferol was predicted to possess the highest binding affinity with both targets.The p53 signaling pathway was predicted to modulate the majority of protein molecules in diabetes mellitus.All the alpha-glucosidase inhibitors were also predicted as membrane integrity agonist and anti-mutagenic compounds.Conclusions:The current study indicates alpha-glucosidase inhibitors from Ficus benghale,nsis can act as aldose reductase inhibitors after absorption from the intestinal tract.Furthermore,these phytoconstituents are involved in the regulation of numerous protein molecules and pathways.Hence,the anti-diabetic efficacies of these compounds are due to their action on multiple protein molecules and synergistic effects which should be confirmed by future investigations.展开更多
Objective:Based on bioinformatics,gene set enrichment analysis(GSEA)and immune infiltration analysis were carried out on the microarray data of psoriasis expression profile to further understand the pathogenesis of ps...Objective:Based on bioinformatics,gene set enrichment analysis(GSEA)and immune infiltration analysis were carried out on the microarray data of psoriasis expression profile to further understand the pathogenesis of psoriasis.Methods:GSE6710 chip data were obtained from gene expression database(GEO),and gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis were performed using GSEA software.22 kinds of immune cell gene expression matrices and R packages were downloaded from CIBERSOFT official website,and the immune cell infiltration matrix was obtained by R software and related graphs were drawn.Results:The pathways related to cell proliferation and innate immunity were highly expressed in psoriatic lesions,and some cancer-related pathways were highly expressed in psoriatic lesions.Immunized cell infiltration analysis showed that activated memory T cells,follicular helper T cells,M0 macrophages and activated dendritic cells were up-regulated in psoriatic skin lesion group,and inactive mast cells were down-regulated in psoriatic skin lesion group.Activated dendritic cells are positively correlated with follicular helper T cells,activated mast cells are positively correlated with M0 macrophages.Inactivated mast cells are negatively correlated with activated memory T cells,M1 macrophages are negatively correlated with regulatory T cells,M0 macrophages are negatively correlated with inactive mast cells.Conclusion:Cell proliferation and innate immunity are of great significance in the pathogenesis of psoriasis.Immune cell infiltration analysis is generally consistent with the current psoriasis pathogenesis model.Macrophages and mast cells also play a certain role in psoriasis.展开更多
It is very important in the field of bioinformatics to apply computer to perform the function annotation for new sequenced bio-sequences. Based on GO database and BLAST program, a novel method for the function annotat...It is very important in the field of bioinformatics to apply computer to perform the function annotation for new sequenced bio-sequences. Based on GO database and BLAST program, a novel method for the function annotation of new biological sequences is presented by using the variable-precision rough set theory. The proposed method is applied to the real data in GO database to examine its effectiveness. Numerical results show that the proposed method has better precision, recall-rate and harmonic mean value compared with existing methods.展开更多
Gene Set Analysis (GSA) is a framework for testing the association of a set of genes and the outcome, e.g. disease status or treatment group. The method replies on computing a maxmean statistic and estimating the null...Gene Set Analysis (GSA) is a framework for testing the association of a set of genes and the outcome, e.g. disease status or treatment group. The method replies on computing a maxmean statistic and estimating the null distribution of the maxmean statistics via a restandardization procedure. In practice, the pre-determined gene sets have stronger intra-correlation than genes across sets. This may result in biases in the estimated null distribution. We derive an asymptotic null distribution of the maxmean statistics based on sparsity assumption. We propose a flexible two group mixture model for the maxmean statistics. The mixture model allows us to estimate the null parameters empirically via maximum likelihood approach. Our empirical method is compared with the restandardization procedure of GSA in simulations. We show that our method is more accurate in null density estimation when the genes are strongly correlated within gene sets.展开更多
目的旨在探讨着丝粒蛋白U(centromere protein U,CENPU)在结直肠癌患者肠组织中的表达情况,并结合生物信息学分析其表达水平对结直肠癌患者预后的影响。方法通过实时荧光定量聚合酶链反应(quantitative real time polymerase chain reac...目的旨在探讨着丝粒蛋白U(centromere protein U,CENPU)在结直肠癌患者肠组织中的表达情况,并结合生物信息学分析其表达水平对结直肠癌患者预后的影响。方法通过实时荧光定量聚合酶链反应(quantitative real time polymerase chain reaction,qRT-PCR)、蛋白质免疫印迹(Western blot,WB)法以及免疫组织化学染色(immunohistochemistry,IHC)实验验证CENPU在组织中的表达情况。结合患者临床病例资料,通过单因素和多因素Cox回归分析CENPU的表达与结直肠癌患者临床病例参数的相关性;然后通过绘制受试操作者操作特征(receiver operating characteristic,ROC)曲线和Kaplan-Meier生存曲线,探究CENPU的表达对结直肠癌患者预后的预测作用。最后,通过生物信息学分析CENPU的表达对结直肠癌疾病进展影响的可能分子机制。结果通过qRT-PCR、WB法以及IHC实验均发现,与正常组织比较,CENPU在结直肠癌患者癌组织中表达显著升高。Cox回归分析表明CENPU的表达与患者的年龄和TNM分期显著相关,是影响患者预后的危险因素。Kaplan-Meier生存曲线分析表明:CENPU高表达的结直肠癌患者的生存率显著降低。ROC曲线结果表明:基于CENPU的表达建立的模型具有较高的预测结直肠癌患者预后的能力。生物信息学分析结果表明:CENPI、CENPN、CENPD、CENPK、CENPP、CENPM、CENPQ、CENPH、NDC80以及ITGB3BP这10个基因与CENPU基因具有相互作用关系;CENPU参与DNA修复、MYC/TARGETS/V1以及PI3K/AKT/MTOR等信号通路。结论结直肠癌患者癌组织中高表达的CENPU与患者的不良预后显著相关,提示CENPU有望成为结直肠癌患者早期诊断及预测预后的潜在靶点。展开更多
目的从通路水平探究慢性阻塞性肺疾病有效方药补肺益肾方的干预机制。方法采用LPS诱导巨噬细胞建立炎症反应模型。基于基因集富集分析(Gene set enrichment analysis,GSEA)方法,筛选巨噬细胞炎症反应相关通路,通过富集评分(Normalized e...目的从通路水平探究慢性阻塞性肺疾病有效方药补肺益肾方的干预机制。方法采用LPS诱导巨噬细胞建立炎症反应模型。基于基因集富集分析(Gene set enrichment analysis,GSEA)方法,筛选巨噬细胞炎症反应相关通路,通过富集评分(Normalized enrichment score,NES)筛选药物干预后发生逆转的通路,揭示补肺益肾方及其配伍的干预机制。结果补肺益肾方所含中药的NES为-1377.23,其中补肾配伍的为-485.07、活血配伍的为-351.86、化痰配伍的为-303.71、益气配伍的为-236.59;补肺益肾方显著逆转的通路为213条,其中活血配伍的为184条、补肾配伍的为147条、化痰配伍的为134条、益气配伍的为133条,逆转率分别为75.41%、60.25%、54.92%、54.51%。TGF-βproduction等90条通路在4个配伍中均被显著逆转。Positive regulation of cytokine production involved in inflammatory response等为配伍特异性逆转通路。结论补肺益肾方各配伍组逆转炎症信号通路的强度依次为补肾、活血、化痰、益气配伍,逆转通路数量依次为活血、补肾、化痰、益气。补肺益肾方可通过调控各配伍共性及特异性逆转通路干预炎症反应。展开更多
基金Projects from China National Department of Science and Technology(81070465)a project from China Jiangsu Province (BM2008151)
文摘Objective:To construct SET gene recombinant adenovirus vector and SET gene small interfering RNA(SiRNA) recombinant adenovirus vector for over-expression or knock-down of SET levels. Methods:The cDNA sequence of SET was cloned by reverse transcriptive polymerase chain reaction(RT-PCR) and the SET gene fragment was subcloned into adenovirus shuttle plasmid pAdTrack-CMV to construct the shuttle plasmid pAdTrack-SET.The shuttle plasmid pAdtrack-SET was transformed into BJ5183 cells with the adenoviral backbone pAdEasy-1 to obtain the homologous recombinant Ad-CMV-SET and the recombinant Ad-CMV-SET was packaged and amplified in the AD293 cells.The expression of SET in AD293 cells was detected by Western blot.In addition,we constructed SET gene SiRNA recombinant adenovirus vector(Ad-H1-SiRNA/SET) and its efficacy of knockdown of SET protein was detected in infected GC-2spd(ts) cells by Western blot. Results:The recombinant adenovirus vectors,both SET gene recombinant adenovirus vector Ad-CMV-SET and SET gene SiRNA recombinant adenovirus vector Ad-H1-SiRNA/SET,were proven to be constructed successfully by the evidence of endonulease digestion and sequencing.AD293 cells infected with either recombinant adenovirus vector of Ad-CMV-SET or Ad-H1-SiRNA/SET were observed to express GFP.The expression of SET protein was up-regulated significantly in AD293 cells infected with SET gene recombinant adenovirus vector.On the contrast, SET protein was significantly down-regulated in the GC-2spd(ts) cells infected with Ad-H1-SiRNA/SET (P<0.05) and the knockdown efficiency was approximately 50%-70%. Conclusion:The recombinant adenovirus vector Ad-CMV-SET and Ad-H1-SiRNA/SET were successfully constructed and effectively expressed in germ cells and somatic cells.It provides an experimental tool for further study of SET gene in the physiological and pathophysiological mechanism of reproduction-related diseases.
文摘Objective:To identify alpha-glucosidase inhibitors from Ficus benghalensis and analyze gene set enrichment of regulated protein molecules.Methods:The phytoconstituents of Ficu.s benghalen.sis were queried for inhibitors of alphaglucosidase,also identified as aldose reductase inhibitors.Druglikeness score,absorption,distribution,metabolism,excretion and toxicity profile,biological spectrum,and gene expression were predicated for each compound.Docking study was performed to predict the binding affinity with alpha-glucosidase and aldose reductase and compared with clinically proven molecules.Kyoto Encyclopedia of Genes and Genomes pathway analysis was performed for the regulated genes to identify the modulated pathways.Results:Apigenin,3,4’,5,7-tetrahydroxy-3’-methoxyflavone,and kaempferol were identified as inhibitors of alpha-glucosidase and aldose reductase.Kaempferol was predicted to possess the highest binding affinity with both targets.The p53 signaling pathway was predicted to modulate the majority of protein molecules in diabetes mellitus.All the alpha-glucosidase inhibitors were also predicted as membrane integrity agonist and anti-mutagenic compounds.Conclusions:The current study indicates alpha-glucosidase inhibitors from Ficus benghale,nsis can act as aldose reductase inhibitors after absorption from the intestinal tract.Furthermore,these phytoconstituents are involved in the regulation of numerous protein molecules and pathways.Hence,the anti-diabetic efficacies of these compounds are due to their action on multiple protein molecules and synergistic effects which should be confirmed by future investigations.
基金Beijing Key Laboratory of Clinical Basic Research on Psoriasis of Traditional Chinese Medicine(No.BZ0375-KF201602)。
文摘Objective:Based on bioinformatics,gene set enrichment analysis(GSEA)and immune infiltration analysis were carried out on the microarray data of psoriasis expression profile to further understand the pathogenesis of psoriasis.Methods:GSE6710 chip data were obtained from gene expression database(GEO),and gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis were performed using GSEA software.22 kinds of immune cell gene expression matrices and R packages were downloaded from CIBERSOFT official website,and the immune cell infiltration matrix was obtained by R software and related graphs were drawn.Results:The pathways related to cell proliferation and innate immunity were highly expressed in psoriatic lesions,and some cancer-related pathways were highly expressed in psoriatic lesions.Immunized cell infiltration analysis showed that activated memory T cells,follicular helper T cells,M0 macrophages and activated dendritic cells were up-regulated in psoriatic skin lesion group,and inactive mast cells were down-regulated in psoriatic skin lesion group.Activated dendritic cells are positively correlated with follicular helper T cells,activated mast cells are positively correlated with M0 macrophages.Inactivated mast cells are negatively correlated with activated memory T cells,M1 macrophages are negatively correlated with regulatory T cells,M0 macrophages are negatively correlated with inactive mast cells.Conclusion:Cell proliferation and innate immunity are of great significance in the pathogenesis of psoriasis.Immune cell infiltration analysis is generally consistent with the current psoriasis pathogenesis model.Macrophages and mast cells also play a certain role in psoriasis.
基金the support of the National Natural Science Foundation of China under Grant No.60673023,60433020,10501017,3040016the European Commission for TH/Asia Link/010 under Grant No.111084.
文摘It is very important in the field of bioinformatics to apply computer to perform the function annotation for new sequenced bio-sequences. Based on GO database and BLAST program, a novel method for the function annotation of new biological sequences is presented by using the variable-precision rough set theory. The proposed method is applied to the real data in GO database to examine its effectiveness. Numerical results show that the proposed method has better precision, recall-rate and harmonic mean value compared with existing methods.
文摘Gene Set Analysis (GSA) is a framework for testing the association of a set of genes and the outcome, e.g. disease status or treatment group. The method replies on computing a maxmean statistic and estimating the null distribution of the maxmean statistics via a restandardization procedure. In practice, the pre-determined gene sets have stronger intra-correlation than genes across sets. This may result in biases in the estimated null distribution. We derive an asymptotic null distribution of the maxmean statistics based on sparsity assumption. We propose a flexible two group mixture model for the maxmean statistics. The mixture model allows us to estimate the null parameters empirically via maximum likelihood approach. Our empirical method is compared with the restandardization procedure of GSA in simulations. We show that our method is more accurate in null density estimation when the genes are strongly correlated within gene sets.
文摘目的旨在探讨着丝粒蛋白U(centromere protein U,CENPU)在结直肠癌患者肠组织中的表达情况,并结合生物信息学分析其表达水平对结直肠癌患者预后的影响。方法通过实时荧光定量聚合酶链反应(quantitative real time polymerase chain reaction,qRT-PCR)、蛋白质免疫印迹(Western blot,WB)法以及免疫组织化学染色(immunohistochemistry,IHC)实验验证CENPU在组织中的表达情况。结合患者临床病例资料,通过单因素和多因素Cox回归分析CENPU的表达与结直肠癌患者临床病例参数的相关性;然后通过绘制受试操作者操作特征(receiver operating characteristic,ROC)曲线和Kaplan-Meier生存曲线,探究CENPU的表达对结直肠癌患者预后的预测作用。最后,通过生物信息学分析CENPU的表达对结直肠癌疾病进展影响的可能分子机制。结果通过qRT-PCR、WB法以及IHC实验均发现,与正常组织比较,CENPU在结直肠癌患者癌组织中表达显著升高。Cox回归分析表明CENPU的表达与患者的年龄和TNM分期显著相关,是影响患者预后的危险因素。Kaplan-Meier生存曲线分析表明:CENPU高表达的结直肠癌患者的生存率显著降低。ROC曲线结果表明:基于CENPU的表达建立的模型具有较高的预测结直肠癌患者预后的能力。生物信息学分析结果表明:CENPI、CENPN、CENPD、CENPK、CENPP、CENPM、CENPQ、CENPH、NDC80以及ITGB3BP这10个基因与CENPU基因具有相互作用关系;CENPU参与DNA修复、MYC/TARGETS/V1以及PI3K/AKT/MTOR等信号通路。结论结直肠癌患者癌组织中高表达的CENPU与患者的不良预后显著相关,提示CENPU有望成为结直肠癌患者早期诊断及预测预后的潜在靶点。
文摘目的从通路水平探究慢性阻塞性肺疾病有效方药补肺益肾方的干预机制。方法采用LPS诱导巨噬细胞建立炎症反应模型。基于基因集富集分析(Gene set enrichment analysis,GSEA)方法,筛选巨噬细胞炎症反应相关通路,通过富集评分(Normalized enrichment score,NES)筛选药物干预后发生逆转的通路,揭示补肺益肾方及其配伍的干预机制。结果补肺益肾方所含中药的NES为-1377.23,其中补肾配伍的为-485.07、活血配伍的为-351.86、化痰配伍的为-303.71、益气配伍的为-236.59;补肺益肾方显著逆转的通路为213条,其中活血配伍的为184条、补肾配伍的为147条、化痰配伍的为134条、益气配伍的为133条,逆转率分别为75.41%、60.25%、54.92%、54.51%。TGF-βproduction等90条通路在4个配伍中均被显著逆转。Positive regulation of cytokine production involved in inflammatory response等为配伍特异性逆转通路。结论补肺益肾方各配伍组逆转炎症信号通路的强度依次为补肾、活血、化痰、益气配伍,逆转通路数量依次为活血、补肾、化痰、益气。补肺益肾方可通过调控各配伍共性及特异性逆转通路干预炎症反应。
