EMA - A R package for Easy Microarray data analysis

<p>Abstract</p> <p>Background</p> <p>The increasing number of methodologies and tools currently available to analyse gene expression microarray data can be confusing for non specialist users.</p> <p>Findings</p> <p>Based on the experience of biostatisticians of Institut Curie, we propose both a clear analysis strategy and a selection of tools to investigate microarray gene expression data. The most usual and relevant existing R functions were discussed, validated and gathered in an easy-to-use R package (EMA) devoted to gene expression microarray analysis. These functions were improved for ease of use, enhanced visualisation and better interpretation of results.</p> <p>Conclusions</p> <p>Strategy and tools proposed in the EMA R package could provide a useful starting point for many microarrays users. EMA is part of Comprehensive R Archive Network and is freely available at <url>http://bioinfo.curie.fr/projects/ema/</url>.</p

Abiotic stress effects on the antioxidative response profile of Albizia julibrissin Durazz. (Fabaceae)

Abiotic stresses (e.g., heavy metals, drought, cold, or combinations) induce oxidative stress with overproduction of reactive oxygen species (ROS). We have investigated the antioxidative responses of Albizia julibrissin Durazz. (silk tree, Fabaceae). Four-month-old plants grown in sand cultures were subjected to various single or sequential treatments involving exposure to cadmium (50-250 mu mol L-1 Cd), lead (1000-5000 mu mol L-1 Pb), chilling at 4 degrees C (CH), or drought (DR), for a period of 7-45 days. Leaf extracts were assayed for glutathione peroxidase (GPX), glutathione-disulfide reductase (GR), catalase (CAT), soluble proline (Pro), ascorbate peroxidase (APX), and guaiacol peroxidase (GUAPX). Cd and Pb accumulation in the leaves was also measured. CAT activity decreased strongly with increasing Pb exposure and after CH. It was also found to be reduced after Cd and DR treatments. GR activity increased highly in nearly all treatments, most strongly at high Cd or Pb, after DR ? CH, and after CH followed by Cd. GUAPX and GPX showed similar trends of increase. APX activity dropped after CH, but increased after low Cd treatment and in CH ? DR sequential stresses. Massive accumulation of soluble Pro occurred after 14-21 days in highly Cd-or Pb-stressed plants. CH or DR acclimation led to some alterations of antioxidative responses, particularly for CAT, GR, and APX. Our data indicate that GSH, GSH-linked redox systems, peroxidases, and Pro are possibly the more important antioxidants under severe stress