共查询到20条相似文献,搜索用时 46 毫秒
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Background
Determining whether a gene is differentially expressed in two different samples remains an important statistical problem. Prior work in this area has featured the use of t-tests with pooled estimates of the sample variance based on similarly expressed genes. These methods do not display consistent behavior across the entire range of pooling and can be biased when the prior hyperparameters are specified heuristically. 相似文献3.
Michael Watson 《BMC bioinformatics》2006,7(1):509
Background
Traditional methods of analysing gene expression data often include a statistical test to find differentially expressed genes, or use of a clustering algorithm to find groups of genes that behave similarly across a dataset. However, these methods may miss groups of genes which form differential co-expression patterns under different subsets of experimental conditions. Here we describe coXpress, an R package that allows researchers to identify groups of genes that are differentially co-expressed. 相似文献4.
Background
Microarrays offer great potential as a platform for molecular diagnostics, testing clinical samples for the presence of numerous biomarkers in highly multiplexed assays. In this study applied to infectious diseases, data from a microarray designed for molecular serotyping of Streptococcus pneumoniae was used, identifying the presence of any one of 91 known pneumococcal serotypes from DNA extracts. This microarray incorporated oligonucleotide probes for all known capsular polysaccharide synthesis genes and required a statistical analysis of the microarray intensity data to determine which serotype, or combination of serotypes, were present within a sample based on the combination of genes detected. 相似文献5.
Background
Recent circadian clock studies using gene expression microarray in two different tissues of mouse have revealed not all circadian-related genes are synchronized in phase or peak expression times across tissues in vivo. Instead, some circadian-related genes may be delayed by 4–8 hrs in peak expression in one tissue relative to the other. These interesting biological observations prompt a statistical question regarding how to distinguish the synchronized genes from genes that are systematically lagged in phase/peak expression time across two tissues. 相似文献6.
Background
There are currently a number of competing techniques for low-level processing of oligonucleotide array data. The choice of technique has a profound effect on subsequent statistical analyses, but there is no method to assess whether a particular technique is appropriate for a specific data set, without reference to external data. 相似文献7.
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Jie Zheng Jan T Svensson Kavitha Madishetty Timothy J Close Tao Jiang Stefano Lonardi 《BMC bioinformatics》2006,7(1):7
Background
Expressed sequence tag (EST) datasets represent perhaps the largest collection of genetic information. ESTs can be exploited in a variety of biological experiments and analysis. Here we are interested in the design of overlapping oligonucleotide (overgo) probes from large unigene (EST-contigs) datasets. 相似文献9.
Cécile Bonnard Claudia L Kleinman Nicolas Rodrigue Nicolas Lartillot 《BMC evolutionary biology》2009,9(1):227
Background
Statistical approaches for protein design are relevant in the field of molecular evolutionary studies. In recent years, new, so-called structurally constrained (SC) models of protein-coding sequence evolution have been proposed, which use statistical potentials to assess sequence-structure compatibility. In a previous work, we defined a statistical framework for optimizing knowledge-based potentials especially suited to SC models. Our method used the maximum likelihood principle and provided what we call the joint potentials. However, the method required numerical estimations by the use of computationally heavy Markov Chain Monte Carlo sampling algorithms. 相似文献10.
Veronica Vinciotti Xiaohui Liu Rolf Turk Emile J de Meijer Peter AC 't Hoen 《BMC bioinformatics》2006,7(1):183-12
Background
The identification of biologically interesting genes in a temporal expression profiling dataset is challenging and complicated by high levels of experimental noise. Most statistical methods used in the literature do not fully exploit the temporal ordering in the dataset and are not suited to the case where temporal profiles are measured for a number of different biological conditions. We present a statistical test that makes explicit use of the temporal order in the data by fitting polynomial functions to the temporal profile of each gene and for each biological condition. A Hotelling T 2-statistic is derived to detect the genes for which the parameters of these polynomials are significantly different from each other. 相似文献11.
Background
Time-course microarray experiments produce vector gene expression profiles across a series of time points. Clustering genes based on these profiles is important in discovering functional related and co-regulated genes. Early developed clustering algorithms do not take advantage of the ordering in a time-course study, explicit use of which should allow more sensitive detection of genes that display a consistent pattern over time. Peddada et al. [1] proposed a clustering algorithm that can incorporate the temporal ordering using order-restricted statistical inference. This algorithm is, however, very time-consuming and hence inapplicable to most microarray experiments that contain a large number of genes. Its computational burden also imposes difficulty to assess the clustering reliability, which is a very important measure when clustering noisy microarray data. 相似文献12.
Yadhu?Kumar Ralf?Westram Sebastian?Behrens Bernhard?Fuchs Frank?Oliver?Gl?ckner Rudolf?Amann Harald?Meier Wolfgang?Ludwig
Background
Taxon specific hybridization probes in combination with a variety of commonly used hybridization formats nowadays are standard tools in microbial identification. A frequently applied technology, fluorescence in situ hybridization (FISH), besides single cell identification, allows the localization and functional studies of the microbial community composition. Careful in silico design and evaluation of potential oligonucleotide probe targets is therefore crucial for performing successful hybridization experiments. 相似文献13.
Background
The virulence of Candida species depends on many environmental conditions. Extracellular pH and concentration of alkali metal cations belong among important factors. Nevertheless, the contribution of transporters mediating the exchange of alkali metal cations for protons across the plasma membrane to the cell salt tolerance and other physiological properties of various Candida species has not been studied so far. 相似文献14.
Comparison of 16S rRNA gene sequences of genus <Emphasis Type="Italic">Methanobrevibacter</Emphasis>
Abhijit?S?Dighe Kamlesh?Jangid José?M?González Vyankatesh?J?Pidiyar Milind?S?Patole Dilip?R?Ranade Yogesh?S?Shouche
Background
The phylogeny of the genus Methanobrevibacter was established almost 25 years ago on the basis of the similarities of the 16S rRNA oligonucleotide catalogs. Since then, many 16S rRNA gene sequences of newly isolated strains or clones representing the genus Methanobrevibacter have been deposited. We tried to reorganize the 16S rRNA gene sequences of this genus and revise the taxonomic affiliation of the isolates and clones representing the genus Methanobrevibacter. 相似文献15.
Stefano Moretti Danitsja van Leeuwen Hans Gmuender Stefano Bonassi Joost van Delft Jos Kleinjans Fioravante Patrone Domenico Franco Merlo 《BMC bioinformatics》2008,9(1):361
Background
In gene expression analysis, statistical tests for differential gene expression provide lists of candidate genes having, individually, a sufficiently low p-value. However, the interpretation of each single p-value within complex systems involving several interacting genes is problematic. In parallel, in the last sixty years, game theory has been applied to political and social problems to assess the power of interacting agents in forcing a decision and, more recently, to represent the relevance of genes in response to certain conditions. 相似文献17.
Xavier Robin Natacha Turck Alexandre Hainard Natalia Tiberti Frédérique Lisacek Jean-Charles Sanchez Markus Müller 《BMC bioinformatics》2011,12(1):77
Background
Receiver operating characteristic (ROC) curves are useful tools to evaluate classifiers in biomedical and bioinformatics applications. However, conclusions are often reached through inconsistent use or insufficient statistical analysis. To support researchers in their ROC curves analysis we developed pROC, a package for R and S+ that contains a set of tools displaying, analyzing, smoothing and comparing ROC curves in a user-friendly, object-oriented and flexible interface. 相似文献18.
Biclustering of gene expression data by non-smooth non-negative matrix factorization 总被引:1,自引:0,他引:1
Pedro Carmona-Saez Roberto D Pascual-Marqui F Tirado Jose M Carazo Alberto Pascual-Montano 《BMC bioinformatics》2006,7(1):78
Background
The extended use of microarray technologies has enabled the generation and accumulation of gene expression datasets that contain expression levels of thousands of genes across tens or hundreds of different experimental conditions. One of the major challenges in the analysis of such datasets is to discover local structures composed by sets of genes that show coherent expression patterns across subsets of experimental conditions. These patterns may provide clues about the main biological processes associated to different physiological states. 相似文献19.
Background
Sequential analysis enables repeated statistical analyses to be performed throughout a trial recruitment period, while maintaining a pre-specified power and type I error. Thus the trial can be stopped as soon as the information accumulated is considered sufficient to reach a conclusion. Sequential tests are easy to use and their statistical properties are especially suitable to trials with very straightforward objectives such as non-comparative phase II trials. We report on a phase II study based on the triangular test (TT) aiming at assessing the effectiveness of azithromycin in preventing Plasmodium vivax relapses. 相似文献20.
Yadhu Kumar Ralf Westram Peter Kipfer Harald Meier Wolfgang Ludwig 《BMC bioinformatics》2006,7(1):240