Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns

<p>Abstract</p> <p>Background</p> <p>DNA microarray technology has had a great impact on muscle research and microarray gene expression data has been widely used to identify gene signatures characteristic of the studied conditions. With the rapid accumulation of muscle microarray data, it is of great interest to understand how to compare and combine data across multiple studies. Meta-analysis of transcriptome data is a valuable method to achieve it. It enables to highlight conserved gene signatures between multiple independent studies. However, using it is made difficult by the diversity of the available data: different microarray platforms, different gene nomenclature, different species studied, etc.</p> <p>Description</p> <p>We have developed a system tool dedicated to muscle transcriptome data. This system comprises a collection of microarray data as well as a query tool. This latter allows the user to extract similar clusters of co-expressed genes from the database, using an input gene list. Common and relevant gene signatures can thus be searched more easily. The dedicated database consists in a large compendium of public data (more than 500 data sets) related to muscle (skeletal and heart). These studies included seven different animal species from invertebrates (<it>Drosophila melanogaster, Caenorhabditis elegans</it>) and vertebrates (<it>Homo sapiens, Mus musculus, Rattus norvegicus, Canis familiaris, Gallus gallus</it>). After a renormalization step, clusters of co-expressed genes were identified in each dataset. The lists of co-expressed genes were annotated using a unified re-annotation procedure. These gene lists were compared to find significant overlaps between studies.</p> <p>Conclusions</p> <p>Applied to this large compendium of data sets, meta-analyses demonstrated that conserved patterns between species could be identified. Focusing on a specific pathology (Duchenne Muscular Dystrophy) we validated results across independent studies and revealed robust biomarkers and new pathways of interest. The meta-analyses performed with MADMuscle show the usefulness of this approach. Our method can be applied to all public transcriptome data.</p

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Radiocristallographie — Analyseur de réseaux

L'appareil présenté ci-dessous permet de construire point par point l'image du réseau réciproque d'un cristal, à partir de l'image déformée obtenue sur un diagramme de Weissenberg. L'analyse du diagramme en est simplifiée en particulier dans les cas de cristaux ayant de grands paramètres et dans le cas où les mesures sont faites au moyen d'un densitomètre.Leguen J.-C., Mazé M., Valette M. Radiocristallographie — Analyseur de réseaux. In: Bulletin de la Société française de Minéralogie et de Cristallographie, volume 89, 4, 1966. pp. 455-457

pHi regulation and ultrastructural analysis in cultured gill cells from freshwater or seawater-adapted trout

International audiencePrimary cultures of gill cells from freshwater and seawater-adapted trout were compared. These cultures, developed from an explant technique, exhibited a similar growth. Ultrastructural comparison between cultured and in situ cells showed that most of the cells in primary culture resembled the so called 'pavement' cells, whereas chloride cells were not observed in the cultured epithelium. Several other cells types, representing a minority of cells in primary culture, were observed (mucous cells, vesicular cells, cells with large dense granules and cells containing lysosomes). Morphological observations of cultured pavement cells from freshwater and seawater trout gills were similar, although the density of cellular organelles in cells was less under freshwater conditions. In addition to the morphological comparison, the regulation of intracellular pH in cultured cells from freshwater and seawater gills was examined. Resting pHi was not different for freshwater or seawater gill cells. A sodium-dependent and amiloride-sensitive mechanism was found in cultured cells. Under the experimental conditions used here, this mechanism was most likely a Na+/H+ antiporter in pavement cells from freshwater and seawater-adapted trout. The comparison of pHi recovery after acidification of cells from freshwater and seawater gills showed that the activity or the number of antiporters was higher for cells from seawater trout gill