共查询到20条相似文献,搜索用时 15 毫秒
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Franck Rapaport Andrei Zinovyev Marie Dutreix Emmanuel Barillot Jean-Philippe Vert 《BMC bioinformatics》2007,8(1):35
Background
Microarrays have become extremely useful for analysing genetic phenomena, but establishing a relation between microarray analysis results (typically a list of genes) and their biological significance is often difficult. Currently, the standard approach is to map a posteriori the results onto gene networks in order to elucidate the functions perturbed at the level of pathways. However, integrating a priori knowledge of the gene networks could help in the statistical analysis of gene expression data and in their biological interpretation. 相似文献2.
Co-expression and promoter content analyses assign a role in biotic and abiotic stress responses to plant natriuretic peptides 总被引:1,自引:0,他引:1
Stuart Meier René Bastian Lara Donaldson Shane Murray Vladimir Bajic Chris Gehring 《BMC plant biology》2008,8(1):24
Background
Plant natriuretic peptides (PNPs) are a class of systemically mobile molecules distantly related to expansins. While several physiological responses to PNPs have been reported, their biological role has remained elusive. Here we use a combination of expression correlation analysis, meta-analysis of gene expression profiles in response to specific stimuli and in selected mutants, and promoter content analysis to infer the biological role of the Arabidopsis thaliana PNP, AtPNP-A. 相似文献3.
Background
The MAQC project demonstrated that microarrays with comparable content show inter- and intra-platform reproducibility. However, since the content of gene databases still increases, the development of new generations of microarrays covering new content is mandatory. To better understand the potential challenges updated microarray content might pose on clinical and biological projects we developed a methodology consisting of in silico analyses combined with performance analysis using real biological samples. 相似文献4.
Background
Time-course microarray experiments are widely used to study the temporal profiles of gene expression. Storey et al. (2005) developed a method for analyzing time-course microarray studies that can be applied to discovering genes whose expression trajectories change over time within a single biological group, or those that follow different time trajectories among multiple groups. They estimated the expression trajectories of each gene using natural cubic splines under the null (no time-course) and alternative (time-course) hypotheses, and used a goodness of fit test statistic to quantify the discrepancy. The null distribution of the statistic was approximated through a bootstrap method. Gene expression levels in microarray data are often complicatedly correlated. An accurate type I error control adjusting for multiple testing requires the joint null distribution of test statistics for a large number of genes. For this purpose, permutation methods have been widely used because of computational ease and their intuitive interpretation. 相似文献5.
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Background
Mycoplasma hominis is associated with pelvic inflammatory disease, bacterial vaginosis, post partum fever, sepsis and infections of the central nervous system often leading to serious conditions. Association with development of female infertility has also been suggested, but different publications present different results. We developed a sensitive and fast diagnostic real-time PCR to test clinical samples from women undergoing laparoscopic examination before fertility treatment. To develop a test for the detection and quantification of M. hominis we selected a housekeeping gene, glyceraldehyde-3-phosphate dehydrogenase (gap), as a target. 相似文献7.
Nadine Grisel Stefan Zoller Marzanna Künzli-Gontarczyk Thomas Lampart Martin Münsterkötter Ivano Brunner Lucien Bovet Jean-Pierre Métraux Christoph Sperisen 《BMC plant biology》2010,10(1):185
Background
Ionic aluminum (mainly Al3+) is rhizotoxic and can be present in acid soils at concentrations high enough to inhibit root growth. Many forest tree species grow naturally in acid soils and often tolerate high concentrations of Al. Previously, we have shown that aspen (Populus tremula) releases citrate and oxalate from roots in response to Al exposure. To obtain further insights into the root responses of aspen to Al, we investigated root gene expression at Al conditions that inhibit root growth. 相似文献8.
Background
Most rapidly evolving gene families are involved in immune responses and reproduction, two biological functions which have been assigned to the carcinoembryonic antigen (CEA) gene family. To gain insights into evolutionary forces shaping the CEA gene family we have analysed this gene family in 27 mammalian species including monotreme and marsupial lineages. 相似文献9.
S.V. Bhave P.V. Shanbhag S.K. Sonawane R.R. Parab G.B. Mahajan 《Letters in applied microbiology》2013,56(5):348-355
An actinomycete wild strain PM0626271 (= MTCC 5447), producing novel antibacterial compounds, was isolated from soil collected from Antarctica. The taxonomic status of the isolate was established by polyphasic approach. Scanning electron microscopy observations and the presence of LL‐Diaminopimelic acid in the cell wall hydrolysate confirmed the genus Streptomyces. Analysis of 16S rRNA gene sequence showed highest sequence similarity to Streptomyces radiopugnans (99%). The phylogenetic tree constructed using near complete 16S rRNA gene sequences of the isolate and closely related strains revealed that although the isolate fell within the S. radiopugnans gene subclade, it was allocated a different branch in the phylogenetic tree, separating it from the majority of the radiopugnans strains. Similar to type strain, S. radiopugnans R97T, the Antarctica isolate displayed thermo tolerance as well as resistance to 60Co gamma radiation, up to the dose of 15 kGy. However, media and salt tolerance studies revealed that, unlike the type strain, this isolate needed higher salinity for its growth. This is the first report of S. radiopugnans isolated from the Antarctica region. The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of Streptomyces radiopugnans MTCC 5447 is JQ723477 .
Significance and Impact of the Study
The study presents the first report of isolation of Streptomyces radiopugnans from Antarctica. To date, there is only one publication regarding S. radiopugnans R97T isolated from radiation‐polluted soil. Like the type strain, Antarctica isolate was thermotolerant and radiotolerant, but in addition, it required salts for growth and did not degrade phenol. We envisaged that metabolic pattern of the same species varies based on acclimatization in its native ecological habitat. Additionally, Antarctica isolate had produced novel antibacterial compounds (patent‐US2012/0156295). The study highlighted that least explored extreme regions like Antarctica are rich resources of novel microbial strains producing novel bioactive compounds. 相似文献10.
Background
α1-antitrypsin (AAT) is one of the major serine proteinase inhibitors controlling proteinases in many biological pathways. There is increasing evidence that AAT is able to exert other than antiproteolytic effects. To further examine this question we compared how various doses of the native (inhibitory) and the polymerised (non-inhibitory) molecular form of AAT affect pro-inflammatory responses in human monocytes, in vitro. Human monocytes isolated from different donors were exposed to the native or polymerised form of AAT at concentrations of 0.01, 0.02, 0.05, 0.1, 0.5 and 1 mg/ml for 18 h, and analysed to determine the release of cytokines and to detect the activity of NF-κB. 相似文献11.
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12.
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Background
Many plant species show induced responses that protect them against exogenous attacks. These responses involve the production of many different bioactive compounds. Plant species belonging to the Brassicaceae family produce defensive glucosinolates, which may greatly influence their favorable nutritional properties for humans. Each responding compound may have its own dynamic profile and metabolic relationships with other compounds. The chemical background of the induced response is therefore highly complex and may therefore not reveal all the properties of the response in any single model. 相似文献14.
Alan F Sasso Sastry S Isukapalli Panos G Georgopoulos 《Theoretical biology & medical modelling》2010,7(1):17
Background
Humans are routinely and concurrently exposed to multiple toxic chemicals, including various metals and organics, often at levels that can cause adverse and potentially synergistic effects. However, toxicokinetic modeling studies of exposures to these chemicals are typically performed on a single chemical basis. Furthermore, the attributes of available models for individual chemicals are commonly estimated specifically for the compound studied. As a result, the available models usually have parameters and even structures that are not consistent or compatible across the range of chemicals of concern. This fact precludes the systematic consideration of synergistic effects, and may also lead to inconsistencies in calculations of co-occurring exposures and corresponding risks. There is a need, therefore, for a consistent modeling framework that would allow the systematic study of cumulative risks from complex mixtures of contaminants. 相似文献15.
Background
Many protein families have undergone functional divergence after gene duplications such that current subgroups of the family carry out overlapping but distinct biological roles. For the protein families with known functional subtypes (a functional split), we developed the software, SplitTester, to identify potential regions that are responsible for the observed distinct functional subtypes within the same protein family. 相似文献16.
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Wilhelm Schönhuber Guenhael Le Bourhis Josselyne Tremblay Rudolf Amann Saulius Kulakauskas 《BMC microbiology》2001,1(1):20-8
Background
Ribosomal RNA molecules are widely used for phylogenetic and in situ identification of bacteria. Nevertheless, their use to distinguish microorganisms within a species is often restricted by the high degree of sequence conservation and limited probe accessibility to the target in fluorescence in situ hybridization (FISH). To overcome these limitations, we examined the use of tmRNA for in situ identification. In E. coli, this stable 363 nucleotides long RNA is encoded by the ssrA gene, which is involved in the degradation of truncated proteins. 相似文献18.
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