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1.
microRNAs are short RNAs that reduce gene expression by binding to their targets. The accurate prediction of microRNA targets is essential to understanding the function of microRNAs. Computational predictions indicate that all human genes may be regulated by microRNAs, with each microRNA possibly targeting thousands of genes. Here we discuss computational methods for identifying mammalian microRNA targets and refining them for further experimental validation. We describe microRNA target prediction resources and procedures and how they integrate with various types of experimental techniques that aim to validate them or further explore their function. We also provide a list of target prediction databases and explain how these are curated. 相似文献
2.
Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms. 总被引:3,自引:0,他引:3
Jeanette Reinartz Eddy Bruyns Jing-Zhong Lin Tim Burcham Sydney Brenner Ben Bowen Michael Kramer Rick Woychik 《Briefings in Functional Genomics and Prot》2002,1(1):95-104
Massively parallel signature sequencing (MPSS) is one of the newest tools available for conducting in-depth expression profiling. MPSS is an open-ended platform that analyses the level of expression of virtually all genes in a sample by counting the number of individual mRNA molecules produced from each gene. There is no requirement that genes be identified and characterised prior to conducting an experiment. MPSS has a routine sensitivity at a level of a few molecules of mRNA per cell, and the datasets are in a digital format that simplifies the management and analysis of the data. Therefore, of the various microarray and non-microarray technologies currently available, MPSS provides many advantages for generating the type of complete datasets that will help to facilitate hypothesis-driven experiments in the era of digital biology. 相似文献
3.
Until recently, the approach to understanding the molecular basis of complex syndromes such as cancer, coronary artery disease, and diabetes was to study the behavior of individual genes. However, it is generally recognized that expression of a number of genes is coordinated both spatially and temporally and that this coordination changes during the development and progression of diseases. Newly developed functional genomic approaches, such as serial analysis of gene expression (SAGE) and DNA microarrays have enabled researchers to determine the expression pattern of thousands of genes simultaneously. One attractive feature of SAGE compared to microarrays is its ability to quantify gene expression without prior sequence information or information about genes that are thought to be expressed. SAGE has been successfully applied to the gene expression profiling of a number of human diseases. In this review, we will first discuss SAGE technique and contrast it to microarray. We will then highlight new biological insights that have emerged from its application to the study of human diseases. 相似文献
4.
Degenkolbe T Hannah MA Freund S Hincha DK Heyer AG Köhl KI 《Analytical biochemistry》2005,346(2):217-224
Gene expression profiling on microarrays is widely used to measure the expression of large numbers of genes in a single experiment. Because of the high cost of this method, feasible numbers of replicates are limited, thus impairing the power of statistical analysis. As a step toward reducing technically induced variation, we developed a procedure of sample preparation and analysis that minimizes the number of sample manipulation steps, introduces quality control before array hybridization, and allows recovery of the prepared mRNA for independent validation of results. Sample preparation is based on mRNA separation using oligo(dT) magnetic beads, which are subsequently used for first-strand cDNA synthesis on the beads. cDNA covalently bound to the magnetic beads is used as template for second-strand cDNA synthesis, leaving the intact mRNA in solution for further analysis. The quality of the synthesized cDNA can be assessed by quantitative polymerase chain reaction using 3'- and 5'-specific primer pairs for housekeeping genes such as glyceraldehyde-3-phosphate dehydrogenase. Second-strand cDNA is chemically labeled with fluorescent dyes to avoid dye bias in enzymatic labeling reactions. After hybridization of two differently labeled samples to microarray slides, arrays are scanned and images analyzed automatically with high reproducibility. Quantile-normalized data from five biological replica display a coefficient of variation 45% for 90% of profiled genes, allowing detection of twofold changes with false positive and false negative rates of 10% each. We demonstrate successful application of the procedure for expression profiling in plant leaf tissue. However, the method could be easily adapted for samples from animal including human or from microbial origin. 相似文献
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6.
建立基于荧光微球的液相基因表达阵列,用于特定基因组合的表达谱分析.采用带有不同强度荧光鉴别信号的羧基化微球,与氨基修饰的不同标签寡核苷酸序列化学偶联,制成微球阵列.多重连接依赖的探针扩增技术(MLPA)用于扩增靶基因核苷酸序列,即通过RNA标本六随机引物逆转成cDNA,与不同基因特异性的一对探针杂交,耐高温的连接酶联接,最后采用生物素标记的同一对引物扩增.PCR产物与微球阵列液相杂交,加入链亲和素标记的PE染料,上流式细胞仪检测.应用这一系统检测骨髓增生异常综合症中难治性贫血(RA)、难治性贫血伴原始细胞增多(RAEB)、难治性贫血伴转化中原始细胞增多(RAEBt)、急性髓细胞性白血病(AML)和其他组(包括再生障碍性贫血、血小板减少、巨幼贫、溶贫等)差异表达谱,差异表达结果用实时荧光定量PCR验证.共建立了5个基因的微球阵列,分别为Rap1GAP、RAC2、SPA1、RhoBTB3和内参GAPDH,每个基因检测的线性范围为0.002 5~0.1μmol,液相表达阵列具有良好的特异性和重复性(P<0.001).检测RA、RAEB、RAEBt、AML和其他组差异表达发现,RAC2、RhoBTB3、SPA-1和Rap1GAP各组间有显著性差异性存在(分别为P<0.000 1,P=0.049 1,P=0.020 6和P=0.004 6),其差异显著性与实时荧光定量PCR一致,泊松相关系数分别为0.930,0.946,0.945和0.921,具显著性(P<0.001).结果表明,成功建立了基于荧光微球的液相基因表达阵列,其敏感性高、特异性强、重复性好. 相似文献
7.
Jumtee K Bamba T Okazawa A Fukusaki E Kobayashi A 《Journal of experimental botany》2008,59(6):1187-1200
In this study, metabolite profiling was demonstrated as a usefultool to plot a specific metabolic pathway, which is regulatedby phytochrome A (phyA). Etiolated Arabidopsis wild-type (WT)and phyA mutant seedlings were irradiated with either far-redlight (FR) or white light (W). Primary metabolites of the irradiatedseedlings were profiled by gas chromatography time-of-flightmass spectrometry (GC/TOF-MS) to obtain new insights on phyA-regulatedmetabolic pathways. Comparison of metabolite profiles in phyAand WT seedlings grown under FR revealed a number of metabolitesthat contribute to the differences between phyA and the WT.Several metabolites, including some amino acids, organic acids,and major sugars, as well as putrescine, were found in smalleramounts in WT compared with the content in phyA seedlings grownunder FR. There were also significant differences between metaboliteprofiles of WT and phyA seedlings during de-etiolation underW. The polyamine biosynthetic pathway was investigated further,because putrescine, one of the polyamines existing in a widevariety of living organisms, was found to be present in loweramounts in WT than in phyA under both light conditions. Theexpression levels of polyamine biosynthesis-related genes wereinvestigated by quantitative real-time RT-PCR. The gene expressionprofiles revealed that the arginine decarboxylase 2 (ADC2) genewas transcribed less in the WT than in phyA seedlings underboth light conditions. This finding suggests that ADC2 is negativelyregulated by phyA during photomorphogenesis. In addition, S-adenosylmethioninedecarboxylase 2 and 4 (SAMDC2 and SAMDC4) were found to be regulatedby phyA but in a different manner from the regulation of ADC2. Key words: Arabidopsis thaliana, gene expression profiling, metabolite profiling, phytochrome A, polyamine biosynthesis
Received 19 October 2007; Revised 17 January 2008 Accepted 18 January 2008 相似文献
8.
Jaszczak K Sazanov AA Sacharczuk M Korczak M Sazanova AL Parada R Malewski T 《Animal genetics》2006,37(3):253-257
In this preliminary study, differentially expressed genes were investigated in cranial tissues from chickens with hereditary exencephaly using cDNA microarrays containing 1,152 genes and expressed sequence tags (ESTs). Genes showing twofold or greater differences at P < 0.05 between affected and normal cranial cells were considered to be candidates for hereditary exencephaly in chicken. Eighteen ESTs (11 known genes/homologues) were upregulated and 108 ESTs (51 known genes/homologues) were downregulated. The EST AL584231 (ROS006C9), orthologous to human MTHFD1, a known candidate gene for human neural tube defects (NTDs), was expressed at the same level both in normal and affected chicken cranial tissues. ESTs AL584253 (ROS006F7, thioredoxin reductase 1) and AL585511 (ROS024H9, thioredoxin), both involved in NTD pathogenic pathways in mice, were downregulated and had mean ratios of 0.41 and 0.04 for expression in affected vs. normal cells respectively. Expression differences of these two ESTs were confirmed by quantitative real-time polymerase chain reaction. These data indicate that ESTs AL584253 and AL585511 are candidates for hereditary exencephaly in chickens. 相似文献
9.
Recent development of gene expression profiling technologies has enabled the large-scale analysis of gene expression changes during disease progression. Frequently, cardiovascular diseases involve complex interactions of multiple cell types over prolonged periods of time. A better understanding of the pathology of cardiovascular diseases and the potential identification of underlying genetic defects are currently being explored by using profiling methodologies in a number of animal and tissue-culture models. 相似文献
10.
Both microRNA (miRNA) and mRNA expression profiles are important methods for cancer type classification. A comparative study of their classification performance will be helpful in choosing the means of classification. Here we evaluated the classification performance of miRNA and mRNA profiles using a new data mining approach based on a novel SVM (Support Vector Machines) based recursive fea- ture elimination (nRFE) algorithm. Computational experiments showed that information encoded in miRNAs is not sufficient to classify cancers; gut-derived samples cluster more accurately when using mRNA expression profiles compared with using miRNA profiles; and poorly differentiated tumors (PDT) could be classified by mRNA expression profiles at the accuracy of 100% versus 93.8% when using miRNA profiles. Furthermore, we showed that mRNA expression profiles have higher capacity in normal tissue classifications than miRNA. We concluded that classification performance using mRNA profiles is superior to that of miRNA profiles in multiple-class cancer classifications. 相似文献
11.
文章旨在建立一种种子序列介导的可控遗传操作—microRNA靶基因指纹图谱(MicroRNA targets fingerprint,MTFP),用于在基因表达检测中筛选与特定microRNA相关的靶基因。在设定上游种子序列的互补序列和下游锚定序列的基础上添加特殊接头,通过反转录和特殊二步PCR将microRNA的靶基因扩增;扩增后的microRNA靶基因在聚丙烯酰胺凝胶电泳中检测其片段大小和表达丰度,用于筛选在不同生理状态或试验条件下特异表达的基因;特定的靶基因序列通过DNA回收和测序方法得到。以miR-203为例,在不同生理状态的山羊皮肤样品中获得了5条大小分别为718 bp(JN709494)、349 bp(JN709495)、243 bp(JN709496)、156 bp(JN709497)和97 bp(JN709498)的靶基因序列。MTFP经济适用、可操作性强,可用于探索microRNA调节的靶基因,或用来评估靶基因的表达谱特征。 相似文献
12.
We have previously shown that a snoRNA-derived microRNA, miR2, in Giardia lamblia potentially regulates the expression of 22 variant surface protein (VSP) genes. Here, we identified another miRNA, miR4, also capable of regulating the expression of several VSPs but derived from an unannotated open reading frame (ORF) rather than a snoRNA, suggesting a canonical miRNA biogenesis pathway in Giardia. miR4 represses expression of a reporter containing two miR4 antisense sequences at the 3' UTR without causing a corresponding decrease in the mRNA level. This repression requires the presence of the Giardia Argonaute protein (GlAgo) and is reversed by 2' O-methylated antisense oligo to miR4, suggesting an RNA-induced silencing complex (RISC)-mediated mechanism. Furthermore, in vivo and in vitro evidence suggested that the Giardia Dicer protein (GlDcr) is required for miR4 biogenesis. Coimmunoprecipitation of miR4 with GlAgo further verified miR4 as a miRNA. A total of 361 potential target sites for miR4 were bioinformatically identified in Giardia, out of which 69 (32.7%) were associated with VSP genes. miR4 reduces the expression of a reporter containing two copies of the target site from VSP (GL50803_36493) at the 3' UTR. Sixteen of the 69 VSP genes were further found to contain partially overlapping miR2 and miR4 targeting sites. Expression of a reporter carrying the two overlapping sites was inhibited by either miR2 or miR4, but the inhibition was neither synergistic nor additive, suggesting a complex mechanism of miRNA regulation of VSP expression and the presence of a rich miRNAome in Giardia. 相似文献
13.
Lu XC Gong HQ Huang ML Bai SL He YB Mao X Geng Z Li SG Wei L Yuwen JS Xu ZH Bai SN 《Plant molecular biology》2006,61(6):845-861
Elucidating the regulatory mechanisms of plant organ formation is an important component of plant developmental biology and
will be useful for crop improvement applications. Plant organ formation, or organogenesis, occurs when a group of primordial
cells differentiates into an organ, through a well-orchestrated series of events, with a given shape, structure and function.
Research over the past two decades has elucidated the molecular mechanisms of organ identity and dorsalventral axis determinations.
However, little is known about the molecular mechanisms underlying the successive processes. To develop an effective approach
for studying organ formation at the molecular level, we generated organ-specific gene expression profiles (GEPs) reflecting
early development in rice stamen. In this study, we demonstrated that the GEPs are highly correlated with early stamen development,
suggesting that this analysis is useful for dissecting stamen development regulation. Based on the molecular and morphological
correlation, we found that over 26 genes, that were preferentially up-regulated during early stamen development, may participate
in stamen development regulation. In addition, we found that differentially expressed genes during early stamen development
are clustered into two clades, suggesting that stamen development may comprise of two distinct phases of pattern formation
and cellular differentiation. Moreover, the organ-specific quantitative changes in gene expression levels may play a critical
role for regulating plant organ formation.
Electronic Supplementary Material Supplementary material is available for this article at
Xiao-Chun Lu, Hua-Qin Gong contributed equally to this work. 相似文献
14.
Carlos Rodrigo Zárate‐ Bladés Vânia Luiza Deperon Bonato Eduardo Lani Volpe da Silveira Marina Oliveira e Paula Cristina Moraes Junta Paula Sandrin‐Garcia Ana Lúcia Fachin Stephano Spanó Mello Renato Sousa Cardoso Fábio Cícero de Sá Galetti Arlete Aparecida Martins Coelho‐Castelo Simone Gusmão Ramos Eduardo Antonio Donadi Elza Tiemi Sakamoto‐Hojo Geraldo Aleixo da Silva Passos Celio Lopes Silva 《The journal of gene medicine》2009,11(1):66-78
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Lin Li Hui Li JiYing Li ShuTu Xu XiaoHong Yang JianSheng Li JianBing Yan 《中国科学:生命科学英文版》2010,53(6):690-700
Lipids play an important role in plants due to their abundance and their extensive participation in many metabolic processes.
Genes involved in lipid metabolism have been extensively studied in Arabidopsis and other plant species. In this study, a total of 1003 maize lipid-related genes were cloned and annotated, including 42
genes with experimental validation, 732 genes with full-length cDNA and protein sequences in public databases and 229 newly
cloned genes. Ninety-seven maize lipid-related genes with tissue-preferential expression were discovered by in silico gene expression profiling based on 1984483 maize Expressed Sequence Tags collected from 182 cDNA libraries. Meanwhile, 70
QTL clusters for maize kernel oil were identified, covering 34.5% of the maize genome. Fifty-nine (84%) QTL clusters co-located
with at least one lipid-related gene, and the total number of these genes amounted to 147. Interestingly, thirteen genes with
kernel-preferential expression profiles fell within QTL clusters for maize kernel oil content. All the maize lipid-related
genes identified here may provide good targets for maize kernel oil QTL cloning and thus help us to better understand the
molecular mechanism of maize kernel oil accumulation. 相似文献
17.
Partha Mukhopadhyay Guy Brock Vasyl Pihur Cynthia Webb M. Michele Pisano Robert M. Greene 《Birth defects research. Part A, Clinical and molecular teratology》2010,88(7):511-534
BACKGROUND: Orofacial development is a multifaceted process involving precise, spatio‐temporal expression of a panoply of genes. MicroRNAs (miRNAs), the largest family of noncoding RNAs involved in gene silencing, represent critical regulators of cell and tissue differentiation. MicroRNA gene expression profiling is an effective means of acquiring novel and valuable information regarding the expression and regulation of genes, under the control of miRNA, involved in mammalian orofacial development. METHODS: To identify differentially expressed miRNAs during mammalian orofacial ontogenesis, miRNA expression profiles from gestation day (GD) ‐12, ‐13 and ‐14 murine orofacial tissue were compared utilizing miRXplore microarrays from Miltenyi Biotech. Quantitative real‐time PCR was utilized for validation of gene expression changes. Cluster analysis of the microarray data was conducted with the clValid R package and the UPGMA clustering method. Functional relationships between selected miRNAs were investigated using Ingenuity Pathway Analysis. RESULTS: Expression of over 26% of the 588 murine miRNA genes examined was detected in murine orofacial tissues from GD‐12–GD‐14. Among these expressed genes, several clusters were seen to be developmentally regulated. Differential expression of miRNAs within such clusters wereshown to target genes encoding proteins involved in cell proliferation, cell adhesion, differentiation, apoptosis and epithelial‐mesenchymal transformation, all processes critical for normal orofacial development. CONCLUSIONS: Using miRNA microarray technology, unique gene expression signatures of hundreds of miRNAs in embryonic orofacial tissue were defined. Gene targeting and functional analysis revealed that the expression of numerous protein‐encoding genes, crucial to normal orofacial ontogeny, may be regulated by specific miRNAs. Birth Defects Research (Part A), 2010. © 2010 Wiley‐Liss, Inc. 相似文献
18.
Cheng F Wang J Peng J Yang J Fu H Zhang X Xue Y Li W Chu Y Jin Q 《FEMS microbiology letters》2007,270(1):12-20
The pH response of Shigella flexneri 2a 301 was identified by gene expression profiling. Gene expression profiles of cells grown in pH 4.5 or 8.6 were compared with the profiles of cells grown at pH 7.0. Differential expression was observed for 307 genes: 97 were acid up-regulated, 102 were acid down-regulated, 91 were base up-regulated, and 86 were base down-regulated. Twenty-seven genes were found to be both acid and base up-regulated, and 29 genes were both acid and base down-regulated. This study showed that (1) the most pH-dependent genes regulate energy metabolism; (2) the RpoS-dependent acid-resistance system is induced, while the glutamate-dependent acid resistance system is not; (3) high pH up-regulates some virulence genes, while low pH down-regulates them, consistent with Shigella infection of the low gut; and (4) several cross-stress response genes are induced by pH changes. These results also illustrate that many unknown genes are significantly regulated under acid or basic conditions, providing researchers with important information to characterize their function. 相似文献
19.
miRNA的生物形成及调控基因表达机制 总被引:1,自引:0,他引:1
微RNA(microRNA,miRNA)通过调节靶基因的表达水平影响细胞分化、增殖、凋亡等特性,在生物的生长发育和疾病发生发展中发挥重要的作用。将miRNA用于基因功能研究,药物靶点验证,基因治疗等领域有非常好的前景。揭示miRNA的生成和加工过程以及miRNA调节靶基因基因表达水平的作用机制对于阐述miRNA在生理病理过程中的作用有重要意义。因此,本文对miRNA的发生,成熟以及作用机制的研究进展作综述。 相似文献
20.
Higurashi H Arai M Watanabe A Igari H Seki N Kamei K Kuriyama T 《Microbiology and immunology》2007,51(4):407-419
Pathogens of the Aspergillus species are frequently seen in deep-seated mycoses. We previously demonstrated that the culture filtrate of Aspergillus fumigatus (CF) has immunosuppressive effects on polymorphonuclear leukocytes (PMNs), which act as the main phagocytes to hyphae of Aspergillus fumigatus (A. fumigatus). But little is known about the gene expression profiles involved in it. Therefore we investigated the changes in gene expression in human PMNs treated with CF or gliotoxin at two time points, using microarray analysis. CF and gliotoxin changed the expression of 548 and 381 genes, respectively. Only 51 genes showed the same expression patterns with the two stimulants, and CF-induced changes in gene expression occurred comparatively earlier than those induced by gliotoxin. Among 31 genes encoding apoptosis, which were up- or down-regulated in this assay, only 3 genes were similarly changed by both kinds of stimulation. Apoptosis was detected and quantified using two apoptosis assays. CF and gliotoxin changed the expessions of only 3 out of 19 regulated genes related to inflammatory mediators and receptors similarly. The up-regulation of the gene encoding annexin 1 (ANXA1), which is known to be involved in extravasation and apoptosis of neutrophils, may play a role in the immunosuppressive effect of A. fumigatus. The difference in expression changes between CF and gliotoxin is presumed to be caused by the interaction among the components of CF and therefore the interaction is an area of interest for further investigation. 相似文献