Impact of the spotted microarray preprocessing method on fold-change compression and variance stability

<p>Abstract</p> <p>Background</p> <p>The standard approach for preprocessing spotted microarray data is to subtract the local background intensity from the spot foreground intensity, to perform a log2 transformation and to normalize the data with a global median or a lowess normalization. Although well motivated, standard approaches for background correction and for transformation have been widely criticized because they produce high variance at low intensities. Whereas various alternatives to the standard background correction methods and to log2 transformation were proposed, impacts of both successive preprocessing steps were not compared in an objective way.</p> <p>Results</p> <p>In this study, we assessed the impact of eight preprocessing methods combining four background correction methods and two transformations (the log2 and the glog), by using data from the MAQC study. The current results indicate that most preprocessing methods produce fold-change compression at low intensities. Fold-change compression was minimized using the Standard and the Edwards background correction methods coupled with a log2 transformation. The drawback of both methods is a high variance at low intensities which consequently produced poor estimations of the p-values. On the other hand, effective stabilization of the variance as well as better estimations of the p-values were observed after the glog transformation.</p> <p>Conclusion</p> <p>As both fold-change magnitudes and p-values are important in the context of microarray class comparison studies, we therefore recommend to combine the Edwards correction with a hybrid transformation method that uses the log2 transformation to estimate fold-change magnitudes and the glog transformation to estimate p-values.</p

Etude du rôle des protéines liant le calcium dans la physiologie cérébelleuse: modification sélective de leur expression dans le cervelet par transgénèse

Doctorat en Sciences médicalesinfo:eu-repo/semantics/nonPublishe

Complete Genome Sequence of an Environmental Bacillus cereus Isolate Belonging to the Bacillus anthracis Clade.

We report here the complete genome sequence of a isolate identified in a soil sample from Namibia. This isolate is closely related to the clade. While the plasmids (500 and 12 kb) carry no detectable virulence gene, the large plasmid shares a 50-kb continuous region similar to plasmid pXO1

Age dependence of strain determinant on mice motor coordination.

Evaluation of motor coordination and motor learning in mice remains a challenge as many factors may interact with the different tests used. Among these factors, genetic background has been reported to be a major determinant of mice performances in motor coordination tests. However, it is not known if the strain dependence of motor coordination and motor learning remains constant through life. In order to assess this point, we tested during 5 days male and female mice of three different strains (NMRI, C57BL/6J, and C57BL/6J x 129OlaHsd) in runway, rotarod, and thin rod tests at juvenile (first day of testing = postnatal day 19) and adult (3 months) age. We found a strong strain effect on motor performances and motor learning at juvenile age (C57BL/6J performing more poorly than the two other strains), whatever the tests used. Interestingly, the C57BL/6J mice were the best performing mice at the adult age. These strain rankings were observed either in male and female groups. These results demonstrate that the strain determinant on mice performances and motor learning is highly age dependent.Comparative StudyJournal ArticleResearch Support, Non-U.S. Gov'tinfo:eu-repo/semantics/publishe

Wnt/ß-catenin signalling is upregulated in the COPD bronchial epithelium

Rationale: Research into pathways that drive COPD pathophysiology are key to unravel novel therapeutic targets. In contrast with the alveolar epithelium, the role of Wnt in the COPD bronchial epithelium (BE) remains unclear. Methods: We performed a targeted RNA sequencing (RNA-seq) of 92 preselected canonical Wnt-related genes in air/liquid interface-reconstituted BE from 47 patients (9 non-smoker controls, 10 smoker controls, 9 mild COPD, 10 moderate COPD and 9 very severe COPD). Quantification of active and total β-catenin was performed in immunostained BE. In addition, a pilot in vitro modulation experiment was carried out using CHIR99021 and XAV939 to activate or inhibit, respectively, the canonical Wnt pathway, to assess its role in broncho-epithelial differentiation. Results: RNA-seq data of Wnt genes was consistent with a global activation of the canonical Wnt pathway in COPD, as evidenced by the upregulation of PORCN, FZD7, CTNNB1, CSNK2A1&2, SOX4, TCF7L2, and MMP2&7 amongst others. This activation was more pronounced in very severe disease. Increased levels of both active and total β-catenin were observed in BE. In the pilot modulation experiment, CHIR99021 strongly inhibited epithelial differentiation for both goblet (SPDEF, MUC5AC) and ciliated cells (FOXJ1, DNAI1&2), as well as epithelial polarization (pIgR), while XAV939 promoted broncho-epithelial polarization. Conclusions: Canonical Wnt signalling is activated in the COPD bronchial epithelium, and could contribute to the COPD airway epithelial phenotype which will be further assessed through modulation experiments and in situ BE laser microdissection

On the many advantages of using the VariantExperiment class to store, exchange and analyze SARS-CoV-2 genomic data and associated metadata

On Friday, 19 March 2021, WHO organized a virtual global workshop highlighting the need for a globally coordinated plan to increase SARS-CoV-2 genetic sequencing capacities to detect SARS-CoV-2 mutations and variants, and to monitor virus genomic evolution worldwide. One week later, in another virtual meeting, it focused on sero epidemiology for SARS-CoV-2 variants of concern and variants of interest. Efficient monitoring of the virus relies on the storage, handling and sharing of the genomic data and the associated metadata. In this manuscript, we demonstrate how the Bioconductor VariantExperiment class addresses these needs, offering a robust and efficient solution to the requirements laid out by the WHO

Combining multiple laser scans of spotted microarrays by means of a two-way ANOVA model

MOTIVATION: Assessment of gene expression on spotted microarrays is based on measurement of fluorescence intensity emitted by hybridized spots. Unfortunately, quantifying fluorescence intensity from hybridized spots does not always correctly reflect gene expression level. Low gene expression levels produce low fluorescence intensities which tend to be confounded with the local background while high gene expression levels produce high fluorescence intensities which rapidly reach the saturation level. Most algorithms that combine data acquired at different voltages of the photomultiplier tube (PMT) assume that a change in scanner setting transforms the intensity measurements by a multiplicative constant. METHODS AND RESULTS: In this paper we introduce a new model of spot foreground intensity which integrates a PMT voltage independent scanner optical bias. This new model is used to implement a "Combining Multiple Scan using a Two-way ANOVA" (CMS2A) method, which is based on a maximum likelihood estimation of the scanner optical bias. After having computed scanner bias, coefficients of the two-way ANOVA model are used for correcting the saturated spots intensities obtained at high PMT voltage by using their counterpart values at lower PMT voltages. The method was compared to state-of-the-art multiple scan algorithms, using data generated from the MAQC study. CMS2A produced fold-changes that were highly correlated with qPCR fold-changes. As the scanner optical bias is accurately estimated within CMS2A, this method allows also avoiding fold-change compression biases whatever the value of this optical bias