共查询到20条相似文献,搜索用时 187 毫秒
1.
Background
In the microarray experiment, many undesirable systematic variations are commonly observed. Normalization is the process of removing such variation that affects the measured gene expression levels. Normalization plays an important role in the earlier stage of microarray data analysis. The subsequent analysis results are highly dependent on normalization. One major source of variation is the background intensities. Recently, some methods have been employed for correcting the background intensities. However, all these methods focus on defining signal intensities appropriately from foreground and background intensities in the image analysis. Although a number of normalization methods have been proposed, no systematic methods have been proposed using the background intensities in the normalization process. 相似文献2.
Background
High throughput gene expression data from spotted cDNA microarrays are collected by scanning the signal intensities of the corresponding spots by dedicated fluorescence scanners. The major scanner settings for increasing the spot intensities are the laser power and the voltage of the photomultiplier tube (PMT). It is required that the expression ratios are independent of these settings. We have investigated the relationships between PMT voltage, spot intensities, and expression ratios for different scanners, in order to define an optimal scanning procedure. 相似文献3.
Kellie J Archer Catherine I Dumur G Scott Taylor Michael D Chaplin Anthony Guiseppi-Elie Geraldine Grant Andrea Ferreira-Gonzalez Carleton T Garrett 《BMC bioinformatics》2007,8(1):447
Background
Recent research examining cross-platform correlation of gene expression intensities has yielded mixed results. In this study, we demonstrate use of a correction factor for estimating cross-platform correlations. 相似文献4.
Jun Wu Qingchao Qiu Lu Xie Joseph Fullerton Jian Yu Yu Shyr Alfred L George Yajun Yi 《BMC bioinformatics》2009,10(1):420
Background
Widespread use of high-throughput techniques such as microarrays to monitor gene expression levels has resulted in an explosive growth of data sets in public domains. Integration and exploration of these complex and heterogeneous data have become a major challenge. 相似文献5.
Stuart D Pepper Emma K Saunders Laura E Edwards Claire L Wilson Crispin J Miller 《BMC bioinformatics》2007,8(1):273
Background
Used alone, the MAS5.0 algorithm for generating expression summaries has been criticized for high False Positive rates resulting from exaggerated variance at low intensities. 相似文献6.
Background
Application of phenetic methods to gene expression analysis proved to be a successful approach. Visualizing the results in a 3-dimentional space may further enhance these techniques. 相似文献7.
Normalization and analysis of DNA microarray data by self-consistency and local regression
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Background
With the advent of DNA hybridization microarrays comes the remarkable ability, in principle, to simultaneously monitor the expression levels of thousands of genes. The quantiative comparison of two or more microarrays can reveal, for example, the distinct patterns of gene expression that define different cellular phenotypes or the genes induced in the cellular response to insult or changing environmental conditions. Normalization of the measured intensities is a prerequisite of such comparisons, and indeed, of any statistical analysis, yet insufficient attention has been paid to its systematic study. The most straightforward normalization techniques in use rest on the implicit assumption of linear response between true expression level and output intensity. We find that these assumptions are not generally met, and that these simple methods can be improved. 相似文献8.
Peter Maye Mary Louise Stover Yaling Liu David W Rowe Shiaoching Gong Alexander C Lichtler 《BMC biotechnology》2009,9(1):20-13
Background
Reporter gene mice are valuable animal models for biological research providing a gene expression readout that can contribute to cellular characterization within the context of a developmental process. With the advancement of bacterial recombination techniques to engineer reporter gene constructs from BAC genomic clones and the generation of optically distinguishable fluorescent protein reporter genes, there is an unprecedented capability to engineer more informative transgenic reporter mouse models relative to what has been traditionally available. 相似文献9.
Background
The use of reverse engineering methods to infer gene regulatory networks by fitting mathematical models to gene expression data is becoming increasingly popular and successful. However, increasing model complexity means that more powerful global optimisation techniques are required for model fitting. The parallel Lam Simulated Annealing (pLSA) algorithm has been used in such approaches, but recent research has shown that island Evolutionary Strategies can produce faster, more reliable results. However, no parallel island Evolutionary Strategy (piES) has yet been demonstrated to be effective for this task. 相似文献10.
Background
Tight clustering arose recently from a desire to obtain tighter and potentially more informative clusters in gene expression studies. Scattered genes with relatively loose correlations should be excluded from the clusters. However, in the literature there is little work dedicated to this area of research. On the other hand, there has been extensive use of maximum likelihood techniques for model parameter estimation. By contrast, the minimum distance estimator has been largely ignored. 相似文献11.
Stephen F Madden Susan B Carpenter Ian B Jeffery Harry Björkbacka Katherine A Fitzgerald Luke A O'Neill Desmond G Higgins 《BMC bioinformatics》2010,11(1):257
Background
MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression by binding to the messenger RNA (mRNA) of protein coding genes. They control gene expression by either inhibiting translation or inducing mRNA degradation. A number of computational techniques have been developed to identify the targets of miRNAs. In this study we used predicted miRNA-gene interactions to analyse mRNA gene expression microarray data to predict miRNAs associated with particular diseases or conditions. 相似文献12.
Luca Corradi Marco Fato Ivan Porro Silvia Scaglione Livia Torterolo 《BMC bioinformatics》2008,9(1):480
Background
Microarray techniques are one of the main methods used to investigate thousands of gene expression profiles for enlightening complex biological processes responsible for serious diseases, with a great scientific impact and a wide application area. Several standalone applications had been developed in order to analyze microarray data. Two of the most known free analysis software packages are the R-based Bioconductor and dChip. The part of dChip software concerning the calculation and the analysis of gene expression has been modified to permit its execution on both cluster environments (supercomputers) and Grid infrastructures (distributed computing). 相似文献13.
Conditional gene expression in the mouse using a Sleeping Beauty gene-trap transposon 总被引:1,自引:0,他引:1
Aron M Geurts Andrew Wilber Corey M Carlson Paul D Lobitz Karl J Clark Perry B Hackett R Scott McIvor David A Largaespada 《BMC biotechnology》2006,6(1):30-15
Background
Insertional mutagenesis techniques with transposable elements have been popular among geneticists studying model organisms from E. coli to Drosophila and, more recently, the mouse. One such element is the Sleeping Beauty (SB) transposon that has been shown in several studies to be an effective insertional mutagen in the mouse germline. SB transposon vector studies have employed different functional elements and reporter molecules to disrupt and report the expression of endogenous mouse genes. We sought to generate a transposon system that would be capable of reporting the expression pattern of a mouse gene while allowing for conditional expression of a gene of interest in a tissue- or temporal-specific pattern. 相似文献14.
Background
The nematode Caenorhabditis elegans has emerged as a powerful system to study biologic questions ranging from development to aging. The generation of transgenic animals is an important experimental tool and allows use of GFP fusion proteins to study the expression of genes of interest or generation of epitope tagged versions of specific genes. Transgenes are often generated by placing a promoter upstream of a reporter gene or cDNA. This often produces a representative expression pattern, but important exceptions have been observed. To better capture the genuine expression pattern and timing, several investigators have modified large pieces of DNA carried by BACs or fosmids for use in the construction of transgenic animals via recombineering. However, these techniques are not in widespread use despite the advantages when compared to traditional approaches. Additionally, some groups have encountered problems with employing these techniques. Hence, we sought identify ways to improve the simplicity and reliability of the procedure. 相似文献15.
16.
17.
Background
Quality-control is an important issue in the analysis of gene expression microarrays. One type of problem is regional bias, in which one region of a chip shows artifactually high or low intensities (or ratios in a two-channel array) relative to the majority of the chip. Current practice in quality assessment for microarrays does not address regional biases. 相似文献18.
Background
Microarray techniques survey gene expressions on a global scale. Extensive biomedical studies have been designed to discover subsets of genes that are associated with survival risks for diseases such as lymphoma and construct predictive models using those selected genes. In this article, we investigate simultaneous estimation and gene selection with right censored survival data and high dimensional gene expression measurements. 相似文献19.
Background
Cloning of genes in expression libraries, such as the yeast two-hybrid system (Y2H), is based on the assumption that the loss of target genes is minimal, or at worst, managable. However, the expression of genes or gene fragments that are capable of interacting with E. coli or yeast gene products in these systems has been shown to be growth inhibitory, and therefore these clones are underrepresented (or completely lost) in the amplified library. 相似文献20.
Junior Barrera Roberto M CesarJr Carlos HumesJr David C MartinsJr Diogo FC Patrão Paulo JS Silva Helena Brentani 《BMC bioinformatics》2007,8(1):169