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RNA sequencing of exosomes secreted by fibroblast and Schwann cells elucidates mechanisms underlying peripheral nerve regeneration 被引量:1
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作者 Xinyang Zhou Yehua Lv +8 位作者 Huimin Xie Yan Li Chang Liu Mengru Zheng Ronghua Wu Songlin Zhou Xiaosong Gu Jingjing Li Daguo Mi 《Neural Regeneration Research》 SCIE CAS CSCD 2024年第8期1812-1821,共10页
Exosomes exhibit complex biological functions and mediate a variety of biological processes,such as promoting axonal regeneration and functional recove ry after injury.Long non-coding RNAs(IncRNAs)have been reported t... Exosomes exhibit complex biological functions and mediate a variety of biological processes,such as promoting axonal regeneration and functional recove ry after injury.Long non-coding RNAs(IncRNAs)have been reported to play a crucial role in axonal regeneration.Howeve r,the role of the IncRNA-microRNAmessenger RNA(mRNA)-competitive endogenous RNA(ceRNA)network in exosome-mediated axonal regeneration remains unclear.In this study,we performed RNA transcriptome sequencing analysis to assess mRNA expression patterns in exosomes produced by cultured fibroblasts(FC-EXOs)and Schwann cells(SCEXOs).Diffe rential gene expression analysis,Gene Ontology analysis,Kyoto Encyclopedia of Genes and Genomes analysis,and protein-protein intera ction network analysis were used to explo re the functions and related pathways of RNAs isolated from FC-EXOs and SC-EXOs.We found that the ribosome-related central gene Rps5 was enriched in FC-EXOs and SC-EXOs,which suggests that it may promote axonal regeneration.In addition,using the miRWalk and Starbase prediction databases,we constructed a regulatory network of ceRNAs targeting Rps5,including 27 microRNAs and five IncRNAs.The ceRNA regulatory network,which included Ftx and Miat,revealed that exsosome-derived Rps5 inhibits scar formation and promotes axonal regeneration and functional recovery after nerve injury.Our findings suggest that exosomes derived from fibro blast and Schwann cells could be used to treat injuries of peripheral nervous system. 展开更多
关键词 ceRNA network EXOSOMES fibroblast cells gene Ontology(GO) kyoto encyclopedia of genes and genomes(kegg) protein-protein interaction(PPI)networks RNA-seq Schwann cells
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Residue Return Effects Outweigh Tillage Effects on Soil Microbial Communities and Functional Genes in Black Soil Region of Northeast China
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作者 WANG Qian JIA Shuxia +6 位作者 LIANG Aizhen CHEN Xuewen ZHANG Shixiu ZHANG Yan Neil B MCLAUGHLIN GAO Yan HUANG Dandan 《Chinese Geographical Science》 SCIE CSCD 2023年第4期679-692,共14页
Conservation tillage as an effective alternative to mitigate soil degradation has attracted worldwide attention,but the influences of conservation tillage on soil microbial community and especially function remain unc... Conservation tillage as an effective alternative to mitigate soil degradation has attracted worldwide attention,but the influences of conservation tillage on soil microbial community and especially function remain unclear.Shotgun metagenomics sequencing was performed to examine the taxonomic and functional community variations of black soils under three tillage regimes,namely no-tillage with residue(maize straw)return(NTS),moldboard plow with residue return(MPS),and moldboard plow without residue return(MPN)in Northeast China.The results revealed:1)Soil bacterial and archaeal communities differed significantly under different tillage regimes in contrast to soil fungal community.2)The overlay of less tillage and residues return under NTS led to unique soil microbial community composition and functional composition.Specifically,in contrast to other treatments,NTS increased the relative abundances of some taxa such as Bradyrhizobium,Candidatus Solibacter,and Reyranella,along with the relative abundances of some taxa such as Sphingomonas,Unclassified Chloroflexi and Nitrososphaera decreased;NTS had a unique advantage of increasing the relative abundances of genes involved in‘ATP-binding cassette(ABC)transporters’and‘quorum sensing(QS)’pathways,while MPN favored the genes involved in‘flagellar assembly’pathway and some metabolic pathways such as‘carbon’and‘glyoxylate and dicarboxylate’and‘selenocompound’metabolisms.3)Significantly different soil bacterial phyla(Acidobacteria,Gemmatimonadetes,and Chloroflexi)and metabolic pathways existed between MPN and another two treatments(NTS and MPS),while did not exist between NTS and MPS.4)Dissolved organic carbon(DOC)and soil bulk density were significantly affected(P<0.05)by tillage and accounted for the variance both in microbial(bacterial)community structure and functional composition.These results indicated that a change in tillage regime from conventional to conservation tillage results in a shift of microbial community and functional genes,and we inferred that residue return played a more prominent role than less tillage in functional shifts in the microbial community of black soils. 展开更多
关键词 NO-TILLAGE microbial community composition kyoto encyclopedia of genes and genomes(kegg)pathways soil properties
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Hub genes and key pathways of traumatic brain injury: bioinformatics analysis and in vivo validation 被引量:7
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作者 Yun-Liang Tang Long-Jun Fang +3 位作者 Ling-Yang Zhong Jian Jiang Xiao-Yang Dong Zhen Feng 《Neural Regeneration Research》 SCIE CAS CSCD 2020年第12期2262-2269,共8页
The exact mechanisms associated with secondary brain damage following traumatic brain injury(TBI)remain unclear;therefore,identifying the critical molecular mechanisms involved in TBI is essential.The m RNA expression... The exact mechanisms associated with secondary brain damage following traumatic brain injury(TBI)remain unclear;therefore,identifying the critical molecular mechanisms involved in TBI is essential.The m RNA expression microarray GSE2871 was downloaded from the Gene Expression Omnibus(GEO)repository.GSE2871 comprises a total of 31 cerebral cortex samples,including two post-TBI time points.The microarray features eight control and seven TBI samples,from 4 hours post-TBI,and eight control and eight TBI samples from 24 hours post-TBI.In this bioinformatics-based study,109 and 66 differentially expressed genes(DEGs)were identified in a Sprague-Dawley(SD)rat TBI model,4 and 24 hours post-TBI,respectively.Functional enrichment analysis showed that the identified DEGs were significantly enriched in several terms,such as positive regulation of nuclear factor-κB transcription factor activity,mitogen-activated protein kinase signaling pathway,negative regulation of apoptotic process,and tumor necrosis factor signaling pathway.Moreover,the hub genes with high connectivity degrees were primarily related to inflammatory mediators.To validate the top five hub genes,a rat model of TBI was established using the weight-drop method,and real-time quantitative polymerase chain reaction analysis of the cerebral cortex was performed.The results showed that compared with control rats,Tnf-α,c-Myc,Spp1,Cxcl10,Ptprc,Egf,Mmp9,and Lcn2 were upregulated,and Fn1 was downregulated in TBI rats.Among these hub genes,Fn1,c-Myc,and Ptprc may represent novel biomarkers or therapeutic targets for TBI.These identified pathways and key genes may provide insights into the molecular mechanisms of TBI and provide potential treatment targets for patients with TBI.This study was approved by the Experimental Animal Ethics Committee of the First Affiliated Hospital of Nanchang University,China(approval No.003)in January 2016. 展开更多
关键词 bioinformatics DEGs differentially expressed genes gene Ontology hub genes inflammation kyoto encyclopedia of genes and genomes molecular mechanism traumatic brain injury
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Bioinformatics analyses of differentially expressed genes associated with spinal cord injury:a microarray-based analysis in a mouse model 被引量:3
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作者 Lei Guo Jing Lv +2 位作者 Yun-Fei Huang Ding-Jun Hao Ji-Jun Liu 《Neural Regeneration Research》 SCIE CAS CSCD 2019年第7期1262-1270,共9页
Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new op... Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new opportunity for investigating diagnosis,treatment,and prognosis of spinal cord injury.However,differentially expressed genes are not consistent among studies,and many key genes and signaling pathways have not yet been accurately studied.GSE5296 was retrieved from the Gene Expression Omnibus DataSet.Differentially expressed genes were obtained using R/Bioconductor software(expression changed at least two-fold;P < 0.05).Database for Annotation,Visualization and Integrated Discovery was used for functional annotation of differentially expressed genes and Animal Transcription Factor Database for predicting potential transcription factors.The resulting transcription regulatory protein interaction network was mapped to screen representative genes and investigate their diagnostic and therapeutic value for disease.In total,this study identified 109 genes that were upregulated and 30 that were downregulated at 0.5,4,and 24 hours,and 3,7,and 28 days after spinal cord injury.The number of downregulated genes was smaller than the number of upregulated genes at each time point.Database for Annotation,Visualization and Integrated Discovery analysis found that many inflammation-related pathways were upregulated in injured spinal cord.Additionally,expression levels of these inflammation-related genes were maintained for at least 28 days.Moreover,399 regulation modes and 77 nodes were shown in the protein-protein interaction network of upregulated differentially expressed genes.Among the 10 upregulated differentially expressed genes with the highest degrees of distribution,six genes were transcription factors.Among these transcription factors,ATF3 showed the greatest change.ATF3 was upregulated within 30 minutes,and its expression levels remained high at28 days after spinal cord injury.These key genes screened by bioinformatics tools can be used as biological markers to diagnose diseases and provide a reference for identifying therapeutic targets. 展开更多
关键词 nerve REgeneRATION spinal cord injury differentially expressed genes BIOINFORMATICS ANALYSES Database for Annotation Visualization and Integrated Discovery ANALYSIS inflammation kyoto encyclopedia of genes and genomes pathway MICROARRAY transcription factors neural REgeneRATION
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Bioinformatic identification of key candidate genes and pathways in axon regeneration after spinal cord injury in zebrafish 被引量:2
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作者 Jia-He Li Zhong-Ju Shi +6 位作者 Yan Li Bin Pan Shi-Yang Yuan Lin-Lin Shi Yan Hao Fu-Jiang Cao Shi-Qing Feng 《Neural Regeneration Research》 SCIE CAS CSCD 2020年第1期103-111,共9页
Zebrafish and human genomes are highly homologous;however,despite this genomic similarity,adult zebrafish can achieve neuronal proliferation,regeneration and functional restoration within 6–8 weeks after spinal cord ... Zebrafish and human genomes are highly homologous;however,despite this genomic similarity,adult zebrafish can achieve neuronal proliferation,regeneration and functional restoration within 6–8 weeks after spinal cord injury,whereas humans cannot.To analyze differentially expressed zebrafish genes between axon-regenerated neurons and axon-non-regenerated neurons after spinal cord injury,and to explore the key genes and pathways of axonal regeneration after spinal cord injury,microarray GSE56842 was analyzed using the online tool,GEO2R,in the Gene Expression Omnibus database.Gene ontology and protein-protein interaction networks were used to analyze the identified differentially expressed genes.Finally,we screened for genes and pathways that may play a role in spinal cord injury repair in zebrafish and mammals.A total of 636 differentially expressed genes were obtained,including 255 up-regulated and 381 down-regulated differentially expressed genes in axon-regenerated neurons.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment results were also obtained.A protein-protein interaction network contained 480 node genes and 1976 node connections.We also obtained the 10 hub genes with the highest correlation and the two modules with the highest score.The results showed that spectrin may promote axonal regeneration after spinal cord injury in zebrafish.Transforming growth factor beta signaling may inhibit repair after spinal cord injury in zebrafish.Focal adhesion or tight junctions may play an important role in the migration and proliferation of some cells,such as Schwann cells or neural progenitor cells,after spinal cord injury in zebrafish.Bioinformatic analysis identified key candidate genes and pathways in axonal regeneration after spinal cord injury in zebrafish,providing targets for treatment of spinal cord injury in mammals. 展开更多
关键词 axonal REgeneRATION differentially expressed genes focal ADHESIONS gene Ontology kyoto encyclopedia of genes and genomes neural REgeneRATION protein-protein interaction network SIGNALING PATHWAY SPECTRIN tight junctions transforming growth factor beta Wnt SIGNALING PATHWAY
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Transcriptomic Analysis of Aflatoxin B1-Regulated Genes in Rat Hepatic Epithelial Cells
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作者 Yang Liu Ji Jing +3 位作者 Li Guanghui Li Junwen Chen Zhaoli Wang Haiyong 《Transactions of Tianjin University》 EI CAS 2014年第6期451-457,共7页
Aflatoxins are the most popular hepatotoxicants. Chronic exposure to aflatoxins leads to a wide variety ofliver diseases, such as hepatocellular carcinoma. In this study, we analyzed the genome wide expression profile... Aflatoxins are the most popular hepatotoxicants. Chronic exposure to aflatoxins leads to a wide variety ofliver diseases, such as hepatocellular carcinoma. In this study, we analyzed the genome wide expression profiles ofaflatoxin B1-induced rat hepatic epithelial cells. The expression of 325, 184 and 199 special genes was altered whenexposed to 0.03, 0.1 and 0.2 μmol/L aflatoxin B1 respectively, and 239 genes were commonly expressed. After thefunctional analysis on these dose-special genes, we determined several key pathways related to hepatotoxicity, such asTGF-beta signaling pathway, tight junction, adherens junction, the regulation of actin cytoskeleton, ErbB signalingpathway, p53 signaling pathway, pathways in cancer and axon guidance. Common genes were mainly associated withfocal adhesion, ECM-receptor interaction, and cell adhesion molecules. Gene ontology annotations showed a goodconcordance with these pathways. The quantitative real-time polymerase chain reaction(PCR) analysis of selectedgenes showed similar patterns in microarrays. The toxicogenomic study provides a better understanding of molecularmechanisms of aflatoxins. 展开更多
关键词 AFLATOXIN MICROARRAY gene ontology kyoto encyclopedia of genes and genomes(kegg) pathway HEPATOTOXICITY
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Role of ESR Pathway Genes in Breast Cancer: A Review
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作者 Deepak Kumar Marilyn Rae Myers +1 位作者 Ussama Al Homsi Valentin Ilyin 《Advances in Breast Cancer Research》 2018年第2期134-186,共53页
Breast cancer is the leading cause of death in women. Prognosis of breast cancer is often pessimistic because the tumors are prone to metastasizing to the bone, brain, and lung. The estrogen signaling receptor (ESR) p... Breast cancer is the leading cause of death in women. Prognosis of breast cancer is often pessimistic because the tumors are prone to metastasizing to the bone, brain, and lung. The estrogen signaling receptor (ESR) pathway contains 39 main genes and proteins which makes it one of the larger signaling pathways. Predominately this pathway and the proteins within are involved in breast growth and development, making it a prospective area of study for breast cancer. While the healthy ESR pathway has been constructed and is well established, a mechanistic model of mutated genes of ESR pathway has not been delved upon. Such mutated models could be utilized for selecting combinational targets for drug therapies, as well as elucidating crosstalk between other pathways and feedback mechanisms. To construct the mutated models of the ESR pathway it is imperative to assess what is currently understood in the literature and what inconsistencies exist in order to resolve them. Without this information, a model of the ESR pathway will be unreliable and likely unproductive. This review is the detailed literature survey of the biological studies performed on ESR pathways genes, and their respective roles in breast cancer. Furthermore, the details mentioned in the review can be beneficial for the integrated study of the ESR pathway genes, which includes, structural and dynamics study of the genes products, to have a holistic understanding of the cancer mechanism. 展开更多
关键词 Estrogen Signaling Receptor (ESR) Pathway Breast Cancer ESR genes MECHANISTIC Modeling Integrated Study kyoto encyclopedia of genes and genomes (kegg) PubMed Literature Survey
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酒精性肝炎自噬关键基因的筛选及生物信息学分析 被引量:2
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作者 袁超 练庆海 +3 位作者 尼贝贝 许燕 张彤 张剑 《器官移植》 CSCD 北大核心 2024年第1期90-101,共12页
目的筛选酒精性肝炎(AH)的自噬关键基因,探讨AH潜在的生物标志物和治疗靶点。方法采用基因表达综合数据库(GEO)中的2个AH基因芯片和从MSigDB、GeneCards数据库中获得的自噬相关数据集,通过加权基因共表达网络分析(WGCNA)获取关键基因。... 目的筛选酒精性肝炎(AH)的自噬关键基因,探讨AH潜在的生物标志物和治疗靶点。方法采用基因表达综合数据库(GEO)中的2个AH基因芯片和从MSigDB、GeneCards数据库中获得的自噬相关数据集,通过加权基因共表达网络分析(WGCNA)获取关键基因。对筛选的关键基因进行基因本体(GO)、京都基因和基因组百科全书(KEGG)功能富集分析,蛋白质相互作用(PPI)分析,免疫浸润分析,构建信使RNA(mRNA)-微小RNA(miRNA)网络,进行酒精性肝病不同分期的自噬相关关键基因的表达差异分析,并进一步通过实时荧光定量逆转录聚合酶链反应(RT-qPCR)在AH患者和小鼠肝脏组织中验证。结果本研究筛选得到了11个与AH自噬相关的基因(EEF1A2、CFTR、SOX4、TREM2、CTHRC1、HSPB8、TUBB3、PRKAA2、RNASE1、MTCL1、HGF),均为上调基因。在AH患者和小鼠肝脏组织中,SOX4、TREM2、HSPB8、PRKAA2在AH组中的相对表达量均高于对照组。结论SOX4、TREM2、HSPB8、PRKAA2可能是AH潜在的生物标志物和治疗靶点。 展开更多
关键词 酒精性肝炎 自噬 关键基因 生物信息学 加权基因共表达网络分析(WGCNA) 基因本体(GO) 京都基因和基因组百科全书(kegg) 蛋白质相互作用(PPI)
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高尿酸血症状态下低度炎症的病理特点研究
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作者 褚梦真 王雨 +4 位作者 林志健 黄晶 刘亚迪 殷晓阳 张冰 《世界中医药》 CAS 北大核心 2024年第13期1881-1888,共8页
目的:探讨高尿酸血症(HUA)状态下低度炎症的病理特点。方法:根据体质量随机将迪法克鹌鹑分为正常组、模型组,每组10只。以普通饲料:酵母浸膏粉=4∶1制备食饵,并以该食饵喂养模型组鹌鹑,正常组鹌鹑则自由饮食饮水。分别于造模第10、20、3... 目的:探讨高尿酸血症(HUA)状态下低度炎症的病理特点。方法:根据体质量随机将迪法克鹌鹑分为正常组、模型组,每组10只。以普通饲料:酵母浸膏粉=4∶1制备食饵,并以该食饵喂养模型组鹌鹑,正常组鹌鹑则自由饮食饮水。分别于造模第10、20、30天检测血清尿酸,血清炎症介质白细胞介素-1β(IL-1β)、IL-33、IL-2、IL-13、IL-8、IL-17、IL-6、IL-10、IL-12/P40、IL-16、IL-21、C反应蛋白(CRP)、粒细胞巨噬细胞集落刺激因子(GM-CSF)、肿瘤坏死因子-α(TNF-α)、趋化因子CC配体2(CCL2)及γ干扰素(IFN-γ)、神经突起生长导向因子2(Netrin-2)、五聚蛋白3(Pentraxin 3),观察各炎症介质强度变化;造模第30天,取鹌鹑肝、回肠、肾各脏器组织,进行HE染色后观察组织病理形态变化;造模第20天,用基因本体(GO)和京都基因与基因组百科全书(KEGG)富集分析差异炎症介质功能及相关信号通路;用Pearson相关性分析方法分析差异炎症介质与血清尿酸水平的相关性。结果:与正常组比较,模型组鹌鹑血清尿酸水平高(P<0.05),以血清IL-17、IL-6、IL-33等为主的白细胞介素类,以IL-8、CCL2为主的趋化因子类,IFN-γ、TNF-α、CRP及GM-CSF水平均升高(P<0.05),而IL-13、IL-10水平降低(P<0.05)。造模第20天,GO/KEGG富集分析结果显示,HUA状态下的低度炎症可能是尿酸代谢靶点群,通过IL-17、Janus激酶信号转导和转录激活因子(JAK-STAT)等信号通路激活、细胞因子-细胞因子间相互作用,从而诱导IL-6、TNF-α等炎症介质产生。2组组织病理变化结果显示,与正常组相比,模型组回肠组织黏膜下层可见炎性细胞浸润,肝、肾组织未见明显差异。差异炎症介质与血清尿酸水平的相关性分析结果显示,鹌鹑血清中IL-6、TNF-α、CRP、IL-33、IL-17、IL-8、IFN-γ、CCL2、GM-CSF、IL-1β、IL-2、IL-6水平均与血清尿酸水平正相关,IL-10、IL-13水平与血清尿酸水平负相关。结论:HUA鹌鹑模型存在低度炎症,该低度炎症可能与尿酸代谢靶点群通过IL-17、JAK-STAT等信号通路的激活以及细胞因子间的相互作用,从而调控IL-6、TNF-α等炎症介质的产生有关。 展开更多
关键词 高尿酸血症 低度炎症 病理特点 鹌鹑 炎症介质 蛋白芯片技术 酶联免疫吸附试验法 基因本体/京都基因与基因组百科全书富集分析
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生物信息综合数据库KEGG的应用 被引量:2
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作者 袁炜 耿辉 +4 位作者 王馨笛 蒿花 王亚军 陈新欢 马茂 《中国循证心血管医学杂志》 2022年第6期669-673,共5页
随着后基因组时代的来临,利用基因表达产物提供的信息,从分子水平理解生物系统的高级功能,如基因导致的各种疾病及表型、作用的信号通路、集成的基因组功能等,是目前亟待解决的问题。近年来,高通量测序技术的进步与完善,产生大量的实用... 随着后基因组时代的来临,利用基因表达产物提供的信息,从分子水平理解生物系统的高级功能,如基因导致的各种疾病及表型、作用的信号通路、集成的基因组功能等,是目前亟待解决的问题。近年来,高通量测序技术的进步与完善,产生大量的实用性基因数据库资源,通过计算机完成基因及其表达产物的功能演绎,利用信息技术提供的结果推测蛋白质交互网络在各种细胞活动起的作用,能够解释高层次、复杂细胞通路及活动的本质。但由于基因数量庞大,作用通路复杂,需要一个整合基因组、化学和系统功能信息的平台,帮助人们快速了解目标基因的相关功能及通路信息。KEGG数据库即是一个综合性的生物信息数据库,通过基因相关信息对通路等数据进行可视化展示,并建立了跨物种基因间的联系,直观全面地了解目标基因对应各种生物活动的内在规律。 展开更多
关键词 生物信息学 kegg 信号通路 基因
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基于网络药理学探讨派特灵治疗尖锐湿疣的作用机制
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作者 隋秀林 徐晓彤 魏淑相 《中国中西医结合皮肤性病学杂志》 CAS 2024年第2期132-137,共6页
目的基于网络药理学研究外用派特灵治疗尖锐湿疣(CA)的作用机制。方法基于网络药理学的方法,经研究表明派特灵是主要由金银花、苦参、白花蛇舌草、鸦胆子、五倍子、蛇床子和大青叶等组成的中药复方制剂,通过中药系统药理学数据库与分析... 目的基于网络药理学研究外用派特灵治疗尖锐湿疣(CA)的作用机制。方法基于网络药理学的方法,经研究表明派特灵是主要由金银花、苦参、白花蛇舌草、鸦胆子、五倍子、蛇床子和大青叶等组成的中药复方制剂,通过中药系统药理学数据库与分析平台(TCMSP)数据库获取派特灵主要组成中药的活性成分与相应靶点;通过GeneCards数据库获得与CA相关的疾病靶点,取其基因与靶点交集制作韦恩图;通过STRING数据库和Cytoscape3.7.1软件共同构建蛋白互作网络(PPI),应用R语言下载安装Bioconductor数据库中的相关R包对交集得到的核心靶点进行相应的基因本体(GO)和京都基因与基因组百科全书(KEGG)富集分析。结果在TCMSP数据库共获取109个活性化合物,主要为β谷甾醇、鸦胆甙、槲皮素等,GeneCards数据库共获取疾病靶点74个,PPI网络分析显示共涉及前列腺素内过氧化物合酶-2(PTGS-2)、B细胞淋巴瘤/白血病-2(BCL-2)、过氧化物酶体增殖物激活受体-γ(PPAR-γ)、血管内皮生长因子-A(VEGF-A)、同期蛋白D1(CCND1)等15个核心蛋白,GO、KEGG富集分析显示派特灵可以通过各类癌症通路、人乳头状瘤病毒(HPV)感染、磷脂酰肌醇3激酶-蛋白激酶B(PI3K-Akt)、人巨细胞病毒感染信号通路等多途径、多靶点作用于CA。结论派特灵通过抗HPV病毒、调节免疫等方面达到治疗CA的目的。 展开更多
关键词 网络药理学:尖锐湿疣 派特灵 基因本体功能富集分析 京都基因与基因组百科全书通路分析
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Transcriptomic and bioinformatics analysis of the mechanism by which erythropoietin promotes recovery from traumatic brain injury in mice
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作者 Weilin Tan Jun Ma +9 位作者 Jiayuanyuan Fu Biying Wu Ziyu Zhu Xuekang Huang Mengran Du Chenrui Wu Ehab Balawi Qiang Zhou Jie Zhang Zhengbu Liao 《Neural Regeneration Research》 SCIE CAS CSCD 2024年第1期171-179,共9页
Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate trau... Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate traumatic brain injury in mice by intrape ritoneal injection of erythro poietin for 3 consecutive days.RNA sequencing detected a total of 4065 differentially expressed RNAs,including 1059 mRNAs,92 microRNAs,799 long non-coding RNAs,and 2115circular RNAs.Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed that the coding and non-coding RNAs that were differentially expressed after traumatic brain injury and treatment with erythropoietin play roles in the axon guidance pathway,Wnt pathway,and MAPK pathway.Constructing competing endogenous RNA networks showed that regulatory relationship between the differentially expressed non-coding RNAs and mRNAs.Because the axon guidance pathway was repeatedly enriched,the expression of Wnt5a and Ephb6,key factors in the axonal guidance pathway,was assessed.Ephb6 expression decreased and Wnt5a expression increased after traumatic brain injury,and these effects were reversed by treatment with erythro poietin.These findings suggest that erythro poietin can promote recove ry of nerve function after traumatic brain injury through the axon guidance pathway. 展开更多
关键词 axon guidance bioinformatics analysis competing endogenous RNA ERYTHROPOIETIN gene Ontology kyoto encyclopedia of genes and genomes non-coding RNA RNA sequencing TRANSCRIPTOMICS traumatic brain injury
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AIF1在急性髓系白血病中的表达及生物信息学分析
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作者 高娅娅 李妙雨 +6 位作者 孙文瑞 贾双双 田彪 肖婉婷 张春燕 冯娟 高广勋 《海南医学院学报》 CAS 北大核心 2024年第7期515-525,共11页
目的:探讨同种异体移植炎症因子-1 (allograft inflammatory factor 1, AIF1)在急性髓系白血病(AML)免疫和预后中的价值。方法:利用生物信息学方法分析AIF1在AML中的表达及其与AML患者生存预后的关系。利用癌症基因组图谱(TCGA)和基因型... 目的:探讨同种异体移植炎症因子-1 (allograft inflammatory factor 1, AIF1)在急性髓系白血病(AML)免疫和预后中的价值。方法:利用生物信息学方法分析AIF1在AML中的表达及其与AML患者生存预后的关系。利用癌症基因组图谱(TCGA)和基因型-组织表达(GTEx)数据分析发现AIF1可能是AML的潜在癌基因,进一步通过功能富集分析、基因集富集分析(GSEA)、蛋白质互作网络(PPI)分析对AIF1进行功能分析。通过Wilcoxon符号秩检验和Logistic回归分析确定AIF1和AML患者临床病理特征之间的关系。通过Cox回归和Kaplan-Meier生存曲线评估AIF1的表达与AML患者总生存期(OS)之间的关系。最后通过qRT-PCR和免疫印迹在AML患者的骨髓样本中验证AIF1的表达。结果:AIF1在AML中高表达,且与不良预后相关。AIF1高表达组总生存期比AIF1低表达组缩短。结论:AIF1在AML中的高表达,其表达与AML患者总体生存相关。提示AIF1可能作为AML患者的潜在不良预后标志物。 展开更多
关键词 AIF1 急性髓系白血病 京都基因与基因组数据库富集分析 疾病本体富集分析
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基于咽部分泌物蛋白质组学分析的术后咽痛机制研究
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作者 李梦鸽 张晨源 +3 位作者 赵子鑫 苏学森 苑昕 田首元 《山西医科大学学报》 CAS 2024年第6期740-745,共6页
目的 筛选术后咽痛(postoperative sore throat, POST)病理过程中的差异表达的蛋白质,探讨POST的发生机制。方法 收集山西医科大学第一医院择期手术行全身麻醉气管插管患者的咽部分泌物20例,根据其术后24 h是否发生咽痛将其分为咽痛组(P... 目的 筛选术后咽痛(postoperative sore throat, POST)病理过程中的差异表达的蛋白质,探讨POST的发生机制。方法 收集山西医科大学第一医院择期手术行全身麻醉气管插管患者的咽部分泌物20例,根据其术后24 h是否发生咽痛将其分为咽痛组(POST组)和非咽痛组(对照组),各10例,并进行蛋白定量分析,筛选出样本中的差异蛋白谱,对差异蛋白进行基因本体论(gene ontology, GO)注释及京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes, KEGG)通路分析。结果 POST组和对照组共同鉴定到3 419个蛋白,显著上调的蛋白有190个,显著下调的蛋白有16个。GO注释提示差异蛋白主要参与细胞的代谢、生物调节过程、应激反应及免疫过程。KEGG富集分析提示差异蛋白主要富集于Wnt、泛素介导的蛋白水解及氧化磷酸化等信号通路。结论 POST涉及的生物学过程较多,其中Wnt信号通路与疼痛关系密切,因此POST可能是通过该通路介导的结果。 展开更多
关键词 术后咽痛 蛋白质组学 WNT信号通路 咽部分泌物 GO注释 kegg富集分析
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Analysis of the autophagy gene expression profile of pancreatic cancer based on autophagy-related protein microtubule-associated protein 1A/1B-light chain 3 被引量:14
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作者 Yan-Hui Yang Yu-Xiang Zhang +3 位作者 Yang Gui Jiang-Bo Liu Jun-Jun Sun Hua Fan 《World Journal of Gastroenterology》 SCIE CAS 2019年第17期2086-2098,共13页
BACKGROUND Pancreatic cancer is a highly invasive malignant tumor. Expression levels of the autophagy-related protein microtubule-associated protein 1 A/1 B-light chain 3(LC3) and perineural invasion(PNI) are closely ... BACKGROUND Pancreatic cancer is a highly invasive malignant tumor. Expression levels of the autophagy-related protein microtubule-associated protein 1 A/1 B-light chain 3(LC3) and perineural invasion(PNI) are closely related to its occurrence and development. Our previous results showed that the high expression of LC3 was positively correlated with PNI in the patients with pancreatic cancer. In this study, we further searched for differential genes involved in autophagy of pancreatic cancer by gene expression profiling and analyzed their biological functions in pancreatic cancer, which provides a theoretical basis for elucidating the pathophysiological mechanism of autophagy in pancreatic cancer and PNI.AIM To identify differentially expressed genes involved in pancreatic cancer autophagy and explore the pathogenesis at the molecular level.METHODS Two sets of gene expression profiles of pancreatic cancer/normal tissue(GSE16515 and GSE15471) were collected from the Gene Expression Omnibus.Significance analysis of microarrays algorithm was used to screen differentially expressed genes related to pancreatic cancer. Gene Ontology(GO) analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis were used to analyze the functional enrichment of the differentially expressed genes. Protein interaction data containing only differentially expressed genes was downloaded from String database and screened. Module mining was carried out by Cytoscape software and ClusterOne plug-in. The interaction relationship between the modules was analyzed and the pivot nodes between the functional modules were determined according to the information of the functional modules and the data of reliable protein interaction network.RESULTS Based on the above two data sets of pancreatic tissue total gene expression, 6098 and 12928 differentially expressed genes were obtained by analysis of genes with higher phenotypic correlation. After extracting the intersection of the two differential gene sets, 4870 genes were determined. GO analysis showed that 14 significant functional items including negative regulation of protein ubiquitination were closely related to autophagy. A total of 986 differentially expressed genes were enriched in these functional items. After eliminating the autophagy related genes of human cancer cells which had been defined, 347 differentially expressed genes were obtained. KEGG pathway analysis showed that the pathways hsa04144 and hsa04020 were related to autophagy. In addition,65 clustering modules were screened after the protein interaction network was constructed based on String database, and module 32 contains the LC3 gene,which interacts with multiple autophagy-related genes. Moreover, ubiquitin C acts as a pivot node in functional modules to connect multiple modules related to pancreatic cancer and autophagy.CONCLUSION Three hundred and forty-seven genes associated with autophagy in human pancreatic cancer were concentrated, and a key gene ubiquitin C which is closely related to the occurrence of PNI was determined, suggesting that LC3 may influence the PNI and prognosis of pancreatic cancer through ubiquitin C. 展开更多
关键词 Pancreatic cancer Autophagy-related PROTEIN microtubule-associated PROTEIN 1A/1B-light chain 3 Perineural invasion gene Ontology ANALYSIS kyoto encyclopedia of genes and genomes pathway ANALYSIS Ubiquitin C
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Different protein expression patterns in rat spinal nerves during wallerian degeneration assessed using isobaric tags for relative and absolute quantitation proteomics profiling 被引量:3
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作者 Shuai Wei Xue-Zhen Liang +12 位作者 Qian Hu Wei-Shan Wang Wen-Jing Xu Xiao-Qing Cheng Jiang Peng Quan-Yi Guo Shu-Yun Liu Wen Jiang Xiao Ding Gong-Hai Han Ping Liu Chen-Hui Shi Yu Wang 《Neural Regeneration Research》 SCIE CAS CSCD 2020年第2期315-323,共9页
Sensory and motor nerve fibers of peripheral nerves have different anatomies and regeneration functions after injury. To gain a clear understanding of the biological processes behind these differences, we used a label... Sensory and motor nerve fibers of peripheral nerves have different anatomies and regeneration functions after injury. To gain a clear understanding of the biological processes behind these differences, we used a labeling technique termed isobaric tags for relative and absolute quantitation to investigate the protein profiles of spinal nerve tissues from Sprague-Dawley rats. In response to Wallerian degeneration, a total of 626 proteins were screened in sensory nerves, of which 368 were upregulated and 258 were downregulated. In addition, 637 proteins were screened in motor nerves, of which 372 were upregulated and 265 were downregulated. All identified proteins were analyzed using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis of bioinformatics, and the presence of several key proteins closely related to Wallerian degeneration were tested and verified using quantitative real-time polymerase chain reaction analyses. The differentially expressed proteins only identified in the sensory nerves were mainly relevant to various biological processes that included cell-cell adhesion, carbohydrate metabolic processes and cell adhesion, whereas differentially expressed proteins only identified in the motor nerves were mainly relevant to biological processes associated with the glycolytic process, cell redox homeostasis, and protein folding. In the aspect of the cellular component, the differentially expressed proteins in the sensory and motor nerves were commonly related to extracellular exosomes, the myelin sheath, and focal adhesion. According to the Kyoto Encyclopedia of Genes and Genomes, the differentially expressed proteins identified are primarily related to various types of metabolic pathways. In conclusion, the present study screened differentially expressed proteins to reveal more about the differences and similarities between sensory and motor nerves during Wallerian degeneration. The present findings could provide a reference point for a future investigation into the differences between sensory and motor nerves in Wallerian degeneration and the characteristics of peripheral nerve regeneration. The study was approved by the Ethics Committee of the Chinese PLA General Hospital, China(approval No. 2016-x9-07) in September 2016. 展开更多
关键词 gene ontology kyoto encyclopedia of genes and genomes ISOBARIC tags for RELATIVE and absolute quantitation motor NERVE PROTEOMICS sensory NERVE spinal NERVE Wallerian degeneration
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Spatiotemporal microRNA profile in peripheral nerve regeneration:miR-138 targets vimentin and inhibits Schwann cell migration and proliferation 被引量:6
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作者 Travis B.Sullivan Litchfield C.Robert +6 位作者 Patrick A.Teebagy Shannon E.Morgan Evan W.Beatty Bryan J.Cicuto Peter K.Nowd Kimberly M.Rieger-Christ David J.Bryan 《Neural Regeneration Research》 SCIE CAS CSCD 2018年第7期1253-1262,共10页
While the peripheral nervous system has regenerative ability,restoration of sufficient function remains a challenge.Vimentin has been shown to be localized in axonal growth fronts and associated with nerve regeneratio... While the peripheral nervous system has regenerative ability,restoration of sufficient function remains a challenge.Vimentin has been shown to be localized in axonal growth fronts and associated with nerve regeneration,including myelination,neuroplasticity,kinase signaling in nerve axoplasm,and cell migration;however,the mechanisms regulating its expression within Schwann cell(SC) remain unexplored.The aim of this study was to profile the spatial and temporal expression profile of micro RNA(mi RNA) in a regenerating rat sciatic nerve after transection,and explore the potential role of mi R-138-5 p targeting vimentin in SC proliferation and migration.A rat sciatic nerve transection model,utilizing a polyethylene nerve guide,was used to investigate mi RNA expression at 7,14,30,60,and 90 days during nerve regeneration.Relative levels of mi RNA expression were determined using microarray analysis and subsequently validated with quantitative real-time polymerase chain reaction.In vitro assays were conducted with cultured Schwann cells transfected with mi RNA mimics and assessed for migratory and proliferative potential.The top seven dysregulated mi RNAs reported in this study have been implicated in cell migration elsewhere,and GO and KEGG analyses predicted activities essential to wound healing.Transfection of one of these,mi RNA-138-5 p,into SCs reduced cell migration and proliferation.mi R-138-5 p has been shown to directly target vimentin in cancer cells,and the luciferase assay performed here in rat Schwann cells confirmed it.These results detail a role of mi R-138-5 p in rat peripheral nerve regeneration and expand on reports of it as an important regulator in the peripheral nervous system. 展开更多
关键词 non-coding RNA neural regeneration nerve guide sciatic nerve transection peripheral nerve injury wound healing gene Ontology processes kyoto encyclopedia of genes and genomes pathways microarray luciferase assay
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Gene and protein expression profiles of olfactory ensheathing cells from olfactory bulb versus olfactory mucosa 被引量:1
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作者 Yuan-Xiang Lan Ping Yang +4 位作者 Zhong Zeng Neeraj Yadav Li-Jian Zhang Li-Bin Wang He-Chun Xia 《Neural Regeneration Research》 SCIE CAS CSCD 2022年第2期440-449,共10页
Olfactory ensheathing cells(OECs) from the olfactory bulb(OB) and the olfactory mucosa(OM) have the capacity to repair nerve injury. However, the difference in the therapeutic effect between OB-derived OECs and OM-der... Olfactory ensheathing cells(OECs) from the olfactory bulb(OB) and the olfactory mucosa(OM) have the capacity to repair nerve injury. However, the difference in the therapeutic effect between OB-derived OECs and OM-derived OECs remains unclear. In this study, we extracted OECs from OB and OM and compared the gene and protein expression profiles of the cells using transcriptomics and non-quantitative proteomics techniques. The results revealed that both OB-derived OECs and OM-derived OECs highly expressed genes and proteins that regulate cell growth, proliferation, apoptosis and vascular endothelial cell regeneration. The differentially expressed genes and proteins of OB-derived OECs play a key role in regulation of nerve regeneration and axon regeneration and extension, transmission of nerve impulses and response to axon injury. The differentially expressed genes and proteins of OM-derived OECs mainly participate in the positive regulation of inflammatory response, defense response, cytokine binding, cell migration and wound healing. These findings suggest that differentially expressed genes and proteins may explain why OB-derived OECs and OM-derived OECs exhibit different therapeutic roles. This study was approved by the Animal Ethics Committee of the General Hospital of Ningxia Medical University(approval No. 2017-073) on February 13, 2017. 展开更多
关键词 biological process cellular component gene gene Ontology kyoto encyclopedia of genes and genomes molecular function olfactory bulb olfactory ensheathing cells olfactory mucosa PROTEIN
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基于网络药理学和分子对接探讨康艾注射液治疗乳腺癌的作用机制 被引量:4
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作者 柯昌虎 王运文 +3 位作者 严慧 冯协和 刘佳玲 李志浩 《安徽医药》 CAS 2023年第1期24-29,I0003,共7页
目的利用网络药理学和分子对接探讨康艾注射液治疗乳腺癌的分子机制。方法该研究起止时间为2021年3—6月。资料来源是通过中药系统药理学数据库与分析平台(TCMSP)、Swiss Target Prediction数据库挖掘康艾注射液的化学成分及靶点,借助Un... 目的利用网络药理学和分子对接探讨康艾注射液治疗乳腺癌的分子机制。方法该研究起止时间为2021年3—6月。资料来源是通过中药系统药理学数据库与分析平台(TCMSP)、Swiss Target Prediction数据库挖掘康艾注射液的化学成分及靶点,借助Uniprot数据库进行基因名称校正,在GeneCards、OMIM数据库中检索乳腺癌疾病的相关靶点,利用Venny 2.1在线软件获取药物与疾病的共同靶点,由Cytoscape 3.7.2绘制药物-成分-靶点-疾病网络,STRING数据库在线绘制蛋白互作网络,基于DAVID数据库对靶点进行基因本体(GO)和京都基因与基因组百科全书(KEGG)富集分析,运用AutoDock Vina软件对康艾注射液的关键的活性成分和作用靶点进行分子对接验证。结果康艾注射液的32个有效成分通过调控125个靶点和104条通路对乳腺癌产生作用,4个关键的化合物分别为异鼠李素、槲皮素、山柰酚、氧化苦参碱,可通过肿瘤抑制蛋白(TP53)、外消旋-α丝氨酸/苏氨酸蛋白激酶(AKT1)、核转录因子激活蛋白-1(JUN)、丝裂原活化蛋白激酶1(MAPK1)、肿瘤坏死因子(TNF)等关键靶蛋白介导癌症途径、TNF、低氧诱导因子-1(HIF-1)、磷脂酰肌醇-3-激酶-丝氨酸/苏氨酸蛋白激酶(PI3K-Akt)、凋亡途径、核苷酸结合寡聚化结构域(NOD)样受体、T细胞受体等信号通路发挥抗乳腺癌作用。分子对接表明筛选的靶点蛋白与有效活性成分具有较好的结合活性。结论康艾注射液治疗乳腺癌具有多成分、多靶点、多途径的作用特点,该研究结果为康艾注射液的临床应用及其机制研究提供了理论依据。 展开更多
关键词 乳腺肿瘤 抗肿瘤药 植物 康艾注射液 网络药理学 分子对接 基因本体(GO) 京都基因与基因组百科全书(kegg)
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On microbial community of Pyropia haitanensis by metagenomic analysis
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作者 Junhao WANG Yunxiang MAO +2 位作者 Guoying DU Xiaojiao LI Xianghai TANG 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2021年第3期1091-1102,共12页
Microorganisms plays an important role in the growth of Pyropia haitanensis.To understand the structural and functional diversity of the microorganism community of P.haitanensis(PH40),the associated metabolic pathway ... Microorganisms plays an important role in the growth of Pyropia haitanensis.To understand the structural and functional diversity of the microorganism community of P.haitanensis(PH40),the associated metabolic pathway network in cluster of orthologous groups(COG)and Kyoto Encyclopedia of Genes and Genomes(KEGG),and carbohydrate-active enzymes(CAZymes)were explored in metagenomic analysis.DNA extraction from gametophytes of P.haitanensis was performed first,followed by library construction,sequencing,preprocessing of sequencing data,taxonomy assignment,gene prediction,and functional annotation.The results show that the predominant microorganisms of P.haitanensis were bacteria(98.98%),and the phylum with the highest abundance was Proteobacteria(54.64%),followed by Bacteroidetes(37.92%).Erythrobacter(3.98%)and Hyunsoonleella jejuensis(1.56%)were the genera and species with the highest abundance of bacteria,respectively.The COG annotation demonstrated that genes associated with microbial metabolism was the predominant category.The results of metabolic pathway annotation show that the ABC transport system and two-component system were the main pathways in the microbial community.Plant growth hormone biosynthesis pathway and multi-vitamin biosynthesis functional units(modules)were the other important pathways.The CAZyme annotation revealed that the starch might be an important carbon source for microorganisms.Glycosyl transferase family 2(GT2)and glycosyl transferase family 3(GT3)were the highly abundant families in glucoside transferase superfamily.Six metagenome-assembled genomes containing enzymes involved in the biosynthesis of cobalamin(vitamin B 12)and indole-3-acetic acid were obtained by binning method.They were confirmed to belong to Rhodobacterales and Rhizobiales,respectively.Our findings provide comprehensive insights into the microorganism community of Pyropia. 展开更多
关键词 P.haitanensis METAgenomIC microbial community cluster of orthologous groups(COG) kyoto encyclopedia of genes and genomes(kegg)pathways carbohydrate-active enzymes(CAZymes)
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