microRNA-223在动脉粥样硬化发生过程中的网络调控机制

microRNA-223(miR-223)是参与动脉粥样硬化（atherosclerosis,AS）炎性调控、细胞生长等通路的微小非编码RNA。本研究系统地探究miR-223及其靶基因的网络调控机制,以便全面理解miR-223在AS中的作用。利用miRNA靶基因预测数据库miRDB、miRmap、TargetScan和miRTarBase获取miR-223的靶基因集。R语言分析基因表达综合数据库（gene expression omnibus,GEO）共享平台动脉粥样硬化斑块差异表达基因集（GSE100927）,筛选出斑块差异表达基因,并与miR-223靶基因集交叉匹配。利用基因本体（gene ontology,GO）及基因组数据库（kyoto encyclopedia of genes and genomes,KEGG）分析研究差异表达基因功能。结果显示,斑块中下调的1 584个差异表达基因与miR-223靶基因交叉匹配得到422个交集mRNA。GO及KEGG富集分析发现miR-223可能通过细胞生长、炎症反应以及血管平滑肌收缩等信号通路调节动脉粥样硬化斑块的发生发展过程。蛋白相互作...     

microRNA155在动脉粥样硬化发生过程中的网络调控机制

动脉粥样硬化(atherosclerosis,AS)是一种慢性进行性的血管炎症性疾病,其发病机制主要包括内皮细胞损伤,脂质浸润及炎症介质分泌等。microRNA155(miR-155)是参与AS炎性调控、免疫和自噬信号等通路的微小非编码RNA。系统性研究miR-155及其靶基因的网络调控机制,能全面理解miR-155在AS中的作用,促进其在临床诊断中的应用开发。利用miRNA靶基因预测数据库miRDB、miRmap和Starbase获取miR-155的靶基因集。R语言分析基因表达综合数据库(gene expression omnibus,GEO)共享平台动脉粥样硬化斑块差异表达基因(GSE24702),筛选出18 076个差异表达基因。利用基因集富集分析(gene set enrichment analysis,GSEA)分析,观察这些差异表达基因共同富集在IL6-JAK-STAT3信号通路、炎症反应和TNFα等炎症信号通路。与miR-155靶基因交叉匹配得到371个交集mRNA,其中159个在动脉粥样硬化斑块中上调,212个在动脉粥样硬化斑块中下调。基因本体(gene ontology,GO)及基因组数据库(kyoto encyclopedia of genes and genomes,KEGG)分析研究基因功能,GO富集分析371个差异基因主要富集炎症和凋亡信号通路的负调控等功能,KEGG分析371个差异基因主要富集TGFβ等炎症信号通路。蛋白相互作用网络(protein-protein interaction networks,PPI)分析获得关键节点基因是ARRB2、FBXO11、SOCS1、FBXO22、FBXO30、KRAS、RNF19A、TRIM32、HERC4、PJA1、RCHY1和DET1。本研究表明,miR-155主要通过调控炎症反应等相关信号通路影响斑块细胞炎症、自噬及凋亡等功能,进而影响动脉粥样硬化的各个进程。     

急性髓系白血病mRNA与非编码RNA差异表达谱及CeRNA调控网络分析

利用GEO数据库(gene expression omnibus database)通过生物信息学分析方法探讨急性髓系白血病(acute myelogenous leukemia,AML)的发病机制。检索GEO数据库中AML相关芯片数据集GSE142698、GSE142699和GSE96535。利用GEO2R分析得到差异mRNAs、miRNAs以及差异lncRNAs。利用在线生物信息学分析工具DAVID对差异mRNAs进行GO富集分析和KEGG通路分析。利用miRWalk数据库预测AML相关miRNAs的靶向mRNAs,利用Spongescan数据库预测AML相关miRNAs的靶向lncRNAs,构建lncRNA-miRNA-mRNA竞争性内源RNA （competing endogenous RNA,ceRNA）调控网络。共筛选出29个显著差异mRNAs、70个显著差异miRNAs和20 005个显著差异lncRNAs。GO富集分析和KEGG通路分析显示,差异表达基因主要涉及蛋白磷酸化、细胞分裂、细胞增殖的负调控、基因表达的正向调节、周期蛋白依赖的丝氨酸/苏氨酸激酶活性的调节等生物过程以及细胞周期、细胞衰老、癌症通路、PI3K-Akt通路等信号通路。将miRWalk数据库预测的靶向mRNAs与差异mRNAs取交集,Spongescan数据库预测的靶向lncRNAs与差异lncRNAs取交集,分别确定了25个mRNAs、6个lncRNAs参与AML相关ceRNA调控网络的构建。结果表明,lncRNAs可能作为关键的ceRNA,通过调控miRNA和相关靶基因参与AML的发生与发展,研究结果为AML诊断和治疗的分子生物学研究提供了新的依据。     

结节性甲状腺肿circRNA-miRNA-mRNA调控网络的构建

基于生物信息分析筛选结节性甲状腺肿中差异表达的环状RNA(circRNA),并揭示circRNA-miRNA-mRNA调控网络在结节性甲状腺肿中的作用。从GEO数据库中检索结节性甲状腺肿组织基因芯片数据,利用R软件筛选出差异表达的circRNA。联合多个生物信息数据库预测差异表达circRNA下游的miRNA及mRNA, 并对靶mRNA进行GO及KEGG富集分析。利用STRING在线数据库及Cytoscape软件筛选核心基因。确定了2个circRNA,42个miRNA及546个mRNA。GO及KEGG富集分析表明靶mRNA主要涉及细胞生长及基因表达调控过程。基于Cytoscape软件筛选出了14个核心基因(SP1、IGF1R、RPS6KB1、SMAD2、SMAD3、SMAD4、VEGFA、CCND1、CDK2、HSPA4、HIF1A、CREB1,NR3C1和STAT5A)。最终基于2个circRNA、11个miRNA和14个核心mRNA构建了circRNA-miRNA-mRNA调控网络。结节性甲状腺肿组织中异常表达的circRNA及相关的circRNA-miRNA-mRNA调控网络可能成为结节性甲状腺肿诊断与治疗的新靶点。     

小儿脓毒症休克相关基因的筛选及网络构建

为探究脓毒症休克与SIRS的差异表达基因及网络的构建,筛选潜在的核心基因,从GEO数据库下载相关基因表达谱GSE26378,数据分为脓毒症休克与SIRS各29个样本,通过在线软件GCBI对其进行标准化及差异基因筛选;对差异基因进行GO分析;基于KEGG进行功能通路分析以及基因信号网络分析;差异基因共表达网络分析。结果表明:两组中总共有1 456个基因被识别为差异基因(P0.05),与SIRS组相比,脓毒症休克组中有条859条下调基因,597条上调基因。GO功能富集分析显示差异基因主要参与了细胞周期、细胞免疫、细胞代谢。KEGG功能通路分析显示差异基因主要参与了MAPK信号通路、P53信号通路、wnt信号通路、细胞凋亡信号通路,细胞周期受体信号通路等。共表达分析发现基因CCNB1、NUSAP1、OIP5、SHCBP1、ZWINT、TOP2A、DLGAP5等位于网络中央部位,而基因信号网络分析发现基因PLCB1、PIK3CA、STAT3、CAMK2D、PRKCB、CREB1位于网络核心。基因芯片分析有助于发现脓毒症休克与SIRS患儿外周血单核细胞在转录组学上的改变,而生物信息学网络分析有助于发现潜在的靶点。     

生物信息学分析筛选结直肠癌靶基因及评估预后价值

为寻找与结直肠癌发展和预后相关的潜在关键基因及信号通路.从美国国立信息中心NCBI的GEO数据库获得结直肠癌基因表达数据集GSE106582,通过PCA对样本进行分组,利用GEO2R进行综合分析,筛选结直肠癌与癌旁对照组的差异表达基因;通过DAVID在线工具对差异表达基因进行GO本体分析和KEGG通路富集分析,初步分析...     

基于RNA-seq的无量山乌骨鸡(Gallus gallus)肝脏脂代谢相关miRNAs的筛选

为研究无量山乌骨鸡(Gallus gallus)肝组织脂代谢相关miRNA (microRNA)在不同发育阶段的表达特征,本研究采集出壳当日(D1)和168日龄(D168)母鸡肝组织样品作为试验材料,利用DNBSEQ平台进行测序,采用DEGseq筛选差异表达的miRNA及其靶基因,随机选取9个差异表达miRNA进行RT-qPCR验证,KEGG通路分类筛选出脂代谢相关miRNA并进行聚类分析,预测脂代谢相关miRNA靶基因并进行GO和KEGG通路功能富集,构建脂代谢相关miRNA和靶基因关联网络。分析结果表明,筛选出106个差异表达miRNAs,包括54个上调miRNA和52个下调miRNA;聚类得到41个脂代谢相关的miRNAs;预测到38个靶基因,对靶基因的功能注释确定主要富集于甘油磷脂代谢、脂肪酸代谢和鞘脂代谢等脂质代谢相关通路,novel-gga-miR2311-5p-DGKZ、 novel-gga-miR2047-3p-ACACA、 novel-gga-miR866-3p-DGKH是脂代谢相关候选miRNA-mRNA关系对。研究提示无量山乌骨鸡肝组织miRNA在不同发育阶段的表...     

基于转录组测序技术进行静原鸡差异miRNA与mRNA的关联分析

为探究静原鸡肌肉组织肌苷酸沉积过程的分子调控机制,本研究以静原鸡胸肌和腿肌组织作为试验材料,通过转录组测序技术,利用生物信息学分析方法筛选出差异表达miRNA及其靶基因.分析结果表明,静原鸡胸肌和腿肌组织的比较组合中有39个差异表达miRNAs(19个显著上调,20个显著下调).通过miRNA-mRNA互作网络分析可知,一个miRNA可以靶向多个mRNA参与调控多个靶基因的表达.GO富集分析表明,候选靶基因的功能主要富集于三个分支的单一生物过程、细胞内和结构分子活性等.KEGG通路注释表明,候选靶基因显著富集到碳代谢、蛋白酶体通路和氨基酸的生物合成等通路中.选取4个差异表达miRNA的与肌苷酸合成和代谢相关的候选靶基因(POLR2C,GMPR,IMPDH2和APRT)进行实时荧光定量PCR验证,结果表明,定量结果与转录组测序结果趋势一致.该研究结果为阐明地方鸡种肌苷酸特异性沉积过程中miRNA介导的靶基因与肉品风味的关系及其表达分析提供理论依据.     

肾透明细胞癌预后相关miRNAs的生物信息学分析

目的寻找可作为肾透明细胞癌（ccRCC）生物标志物的miRNA,以及ccRCC与正常组织间miRNA差异表达情况。 方法利用TCGA数据库下载ccRCC中miRNA表达数据,分析肿瘤与正常组织间差异表达miRNA。使用Kaplan-Meier曲线对患者进行生存分析,筛选出表达情况与临床预后相关的miRNA。通过生物信息学对miRNA的靶基因进行预测,然后运用FunRich软件和ClueGO对靶基因进行GO和KEGG富集分析。 结果通过TCGA数据库分析发现,ccRCC较正常组织差异表达miRNA共54个,其中上调33个,下调21个。通过生存分析发现hsa-miR-21和hsa-miR-155与患者预后相关,P≤0.05。进一步通过Perl软件在Targetscan、miRDB、miRTarBase、miRPath这四个数据库中预测miRNA靶基因并将结果取交集,共发现129个靶基因。GO和KEGG分析结果表明,这些靶基因主要与转录因子活性、信号转导以及FoxO、TNF等信号通路密切相关。 结论通过生物信息学分析发现了ccRCC与正常组织的差异表达miRNA;其中hsa-miR-21和hsa-miR-155与患者总体生存率相关,并通过调控靶基因参与相关的信号通路进而影响ccRCC的发生发展进程,提示hsa-miR-21和hsa-miR-155可能是ccRCC潜在的生物标志物。     

应用高通量测序技术检测与奶牛乳产量和乳质量调控相关的miRNA

本实验将中国荷斯坦牛泌乳期高乳品质奶牛（H）和泌乳期低乳品质奶牛（L）乳腺组织作为实验对象,利用高通量测序技术进行了miRNA测序,与miRNA数据库比对,获得已知miRNA,整合miREvo和mirDeep2这两个miRNA预测软件,进行新miRNA分析,通过差异表达分析筛选组间差异miRNAs,获得56个差异表达miRNA(P <0.05,FDRq <0.05)并对差异表达miRNA进行靶基因预测;利用DAVID对靶基因进行GO(Gene Ontology)和信号通路富集分析。经过对靶基因筛选,发现了4个已报道与乳蛋白、乳脂紧密相关的功能基因：CSN3、SCD、LALBA和DGAT2。靶基因聚集的生物学功能多数参与了蛋白质和脂肪代谢,乳腺发育和分化,以及免疫功能。靶基因主要富集在MAPK 信号通路、甘油磷酸脂质代谢、缺氧诱导因子1和磷脂酰肌醇3激酶 蛋白激酶B信号转导通路。结果显示,靶基因主要富集在糖类代谢、脂肪代谢、蛋白质代谢、细胞凋亡以及免疫相关通路。     

应用GSEA和WGCNA方法分析细菌性败血症宿主关键差异基因及意义

【目的】采用生物信息学方法分析公共数据库来源的细菌性败血症患者全血转录组学表达谱,探讨细菌败血症相关的宿主关键差异基因及意义。【方法】基于GEO数据库中GSE80496和GSE72829全血转录组基因数据集,采用GEO2R、基因集富集分析(GSEA)联用加权基因共表达网络分析(WGCNA)筛选细菌性败血症患者相比健康人群显著改变的差异基因,通过R软件对交集基因进行GO功能分析和KEGG富集分析。同时,通过String 11.0和Cytoscape分析枢纽基因,验证枢纽基因在数据集GSE72809(Health组52例,Definedsepsis组52例)全血标本中的表达情况,并探讨婴儿性别、月(胎)龄、出生体重、是否接触抗生素等因素与靶基因表达谱间的关系。【结果】分析GSE80496和GSE72829数据集分别筛选得到932个基因和319个基因,联合WGCNA枢纽模块交集得到与细菌性败血症发病相关的10个枢纽基因(MMP9、ITGAM、CSTD、GAPDH、PGLYRP1、FOLR3、OSCAR、TLR5、IL1RN和TIMP1);GSEA分析获得关键通路(氨基酸糖类-核糖代谢、PPAR信号通路、聚糖生物合成通路、自噬调控通路、补体、凝血因子级联反应、尼古丁和烟酰胺代谢、不饱和脂肪酸生物合成和阿尔兹海默症通路)及生物学过程(类固醇激素分泌、腺苷酸环化酶的激活、细胞外基质降解和金属离子运输)。【结论】本项研究通过GEO2R、GSEA联用WGCNA分析,筛选出与细菌性败血症发病相关的2个枢纽模块、10个枢纽基因以及一些关键信号通路和生物学过程,可为后续深入研究细菌性败血症致病机制奠定理论依据。     

肾透明细胞癌Caki-1细胞系差异表达基因的生物信息学分析

目的比较肾透明细胞癌Caki-1细胞系与正常肾上皮细胞系ASE-5063中的差异表达基因（DEGs）,寻找潜在的肾透明细胞癌特异性分子标志物。 方法利用GEO数据库自带的GEO2R在线分析工具分析基因芯片GSE78179,将筛选出的DEGs分别导入Metascape、STRING以及Cytoscape进行综合分析并筛选出核心基因。最后使用FunRich等软件对筛选出的核心基因进行GO和KEGG富集分析。 结果共筛选出562个DEGs,其中上调基因345个,下调基因217个。进一步使用MCODE筛选出36个关键基因,GO功能分析发现这些基因与细胞粘附分子活性、趋化因子活性、细胞通讯和信号转导等密切相关;KEGG通路富集结果则表明差异基因主要集中在趋化因子信号通路、TNF信号通路以及NF-κB信号通路等多种与肿瘤相关的通路上。 结论运用生物信息学方法筛选出肾透明细胞癌Caki-1细胞系中DEGs,其中数个核心基因广泛参与多种肿瘤的病理进程,但尚未在肾透明细胞癌有相关研究报道,提示其可能是治疗肾透明细胞癌的潜在靶点。     

Identification of differentially expressed genes and biological characteristics of colorectal cancer by integrated bioinformatics analysis

Colorectal cancer (CRC) ranks as one of the most common malignant tumors worldwide. Its mortality rate has remained high in recent years. Therefore, the aim of this study was to identify significant differentially expressed genes (DEGs) involved in its pathogenesis, which may be used as novel biomarkers or potential therapeutic targets for CRC. The gene expression profiles of GSE21510, GSE32323, GSE89076, and GSE113513 were downloaded from the Gene Expression Omnibus (GEO) database. After screening DEGs in each GEO data set, we further used the robust rank aggregation method to identify 494 significant DEGs including 212 upregulated and 282 downregulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed by DAVID and the KOBAS online database, respectively. These DEGs were shown to be significantly enriched in different cancer-related functions and pathways. Then, the STRING database was used to construct the protein–protein interaction network. The module analysis was performed by the MCODE plug-in of Cytoscape based on the whole network. We finally filtered out seven hub genes by the cytoHubba plug-in, including PPBP, CCL28, CXCL12, INSL5, CXCL3, CXCL10, and CXCL11. The expression validation and survival analysis of these hub genes were analyzed based on The Cancer Genome Atlas database. In conclusion, the robust DEGs associated with the carcinogenesis of CRC were screened through the GEO database, and integrated bioinformatics analysis was conducted. Our study provides reliable molecular biomarkers for screening and diagnosis, prognosis as well as novel therapeutic targets for CRC.     

Identification of core genes and outcomes in hepatocellular carcinoma by bioinformatics analysis

Hepatocellular carcinoma (HCC) is the most common malignant liver disease in the world. However, the mechanistic relationships among various genes and signaling pathways are still largely unclear. In this study, we aimed to elucidate potential core candidate genes and pathways in HCC. The expression profiles GSE14520, GSE25097, GSE29721, and GSE62232, which cover 606 tumor and 550 nontumour samples, were downloaded from the Gene Expression Omnibus (GEO) database. Furthermore, HCC RNA-seq datasets were also downloaded from the Cancer Genome Atlas (TCGA) database. The differentially expressed genes (DEGs) were filtered using R software, and we performed gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis using the online databases DAVID 6.8 and KOBAS 3.0. Furthermore, the protein-protein interaction (PPI) network complex of these DEGs was constructed by Cytoscape software, the molecular complex detection (MCODE) plug-in and the online database STRING. First, a total of 173 DEGs (41 upregulated and 132 downregulated) were identified that were aberrantly expressed in both the GEO and TCGA datasets. Second, GO analysis revealed that most of the DEGs were significantly enriched in extracellular exosomes, cytosol, extracellular region, and extracellular space. Signaling pathway analysis indicated that the DEGs had common pathways in metabolism-related pathways, cell cycle, and biological oxidations. Third, 146 nodes were identified from the DEG PPI network complex, and two important modules with a high degree were detected using the MCODE plug-in. In addition, 10 core genes were identified, TOP2A, NDC80, FOXM1, HMMR, KNTC1, PTTG1, FEN1, RFC4, SMC4, and PRC1. Finally, Kaplan-Meier analysis of overall survival and correlation analysis were applied to these genes. The abovementioned findings indicate that the identified core genes and pathways in this bioinformatics analysis could significantly enrich our understanding of the development and recurrence of HCC; furthermore, these candidate genes and pathways could be therapeutic targets for HCC treatment.     

Identification of hub genes and pathways in adrenocortical carcinoma by integrated bioinformatic analysis

Adrenocortical carcinoma (ACC), a rare malignant neoplasm originating from adrenal cortical cells, has high malignancy and few treatments. Therefore, it is necessary to explore the molecular mechanism of tumorigenesis, screen and verify potential biomarkers, which will provide new clues for the treatment and diagnosis of ACC. In this paper, three gene expression profiles (GSE10927, GSE12368 and GSE90713) were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were obtained using the Limma package. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched by DAVID. Protein‐protein interaction (PPI) network was evaluated by STRING database, and PPI network was constructed by Cytoscape. Finally, GEPIA was used to validate hub genes’ expression. Compared with normal adrenal tissues, 74 up‐regulated DEGs and 126 down‐regulated DEGs were found in ACC samples; GO analysis showed that up‐regulated DEGs were enriched in organelle fission, nuclear division, spindle, et al, while down‐regulated DEGs were enriched in angiogenesis, proteinaceous extracellular matrix and growth factor activity; KEGG pathway analysis showed that up‐regulated DEGs were significantly enriched in cell cycle, cellular senescence and progesterone‐mediated oocyte maturation; Nine hub genes (CCNB1, CDK1, TOP2A, CCNA2, CDKN3, MAD2L1, RACGAP1, BUB1 and CCNB2) were identified by PPI network; ACC patients with high expression of 9 hub genes were all associated with worse overall survival (OS). These hub genes and pathways might be involved in the tumorigenesis, which will offer the opportunities to develop the new therapeutic targets of ACC.     

利用RNA-seq数据分析肝细胞癌差异表达基因及蛋白相互作用

RNA-Seq已成为当前转录组学研究的强有力工具,尤其在肿瘤差异表达基因的筛选方面有重要的应用价值。为进一步阐明肝细胞癌(HCC)的分子机制,本研究对GEO中1个包括12对HCC组织标本的RNA-Seq数据集(GSE63863)进行了生物信息学分析。采用edgeR、DESeq2、voom等3种不同算法的软件进行统计分析,共获得976个差异表达基因(adj. p-value<0.01或FDR<0.01,|logFC|≥2),其中上调表达422个(43.2%),下调554个(56.8%)。GO富集分析显示这些差异表达基因主要涉及离子结合、氧化还原酶活性等分子功能以及氧化还原、细胞分裂等生物学过程;KEGG通路分析显示,这些差异表达基因主要涉及细胞周期、视黄醇等代谢通路。STRING分析显示,共有654个基因编码的蛋白质存在相互作用,进一步利用MCODE分析显示,169个基因编码蛋白构成4个子网络,相应的中心节点基因分别为UBE2C、GNG4、TTR、FOS,这些基因的异常表达可能在HCC的发生发展过程中具有重要作用。上述研究结果将为进一步阐明HCC分子发病机制、寻找新型生物标志物提供初步的依据。