DNA Micro-arrays

  HEADDr COPPEE Jean-Yves / jycoppee@pasteur.fr
  MEMBERSDr BISCHOFF Emmanuel / Dr DILLIES Marie-Agnès / Dr JACQUELIN Béatrice
PROUX Caroline / RÉGNAULT Béatrice

  Annual Report

The DNA microarrays platform (PF2) started its activities in 2000. It was initially dedicated to the development of microarrays (glass slide arrays) and macroarrays (nylon membrane arrays) for gene expression profiling and comparative genomics of model microorganisms and pathogens. Since 2003, the platform is also able to deal with projects based on the Affymetrix technology aiming at studies centered on higher eukaryotes. In 2006, PF2 has been involved in 10 macro/microarrays projects and 12 Affymetrix projects. These projects were selected by steering committees following internal calls for proposals and are mainly long-term (several months to years) collaborations. The platform is also collaborating with teams from the International Network of Pasteur Institutes and has established collaborations with several non-Pasteurian teams.

The complete list of all these projects is available on the website of the platform. The projects centered on model microorganisms and pathogens notably concern Legionella pneumophila, Candida glabrata, Entamoeba histolytica, Plasmodium falciparum and Streptomyces lividans. The projects dedicated to higher eukaroytes (human and mouse) mainly concern the host responses to infection and developmental biology.

These projects aim at answering the following biological questions:

- study of virulence factors

- inter-species transcriptome comparison

- study of host-pathogen interactions

- study of the effects of environmental pressures (stress, immune pressure, drug pressure...) on the pathogen

- identification of regulator targets (virulence, motility...)

For the selected projects, the platform is in charge of the preparation of the chips as well as of training needed for the use of the chips and analysis of results. For the projects based on the Affymetrix technology, the PF is also in charge of labelling and hybridization reactions. Data analysis and handling represent 40 % of the activities of the platform. paragraphSeveral tools allowing normalization of the data and their statistical analysis are developed and installed at the platform. We are essentially working with the R environment (Bioconductor) and with several commercial softwares for data mining and interpretation (Arrayminer, S-Plus-ArrayAnalyzer, Ingenuity, Genomatix...)

All equipments and softwares needed for the use and the analysis of the chips are freely accessible for the whole campus. This functioning mode allows the development of strong interactions between the PF and the teams with which we are collaborating.

The platform also has some training activities. In 2006, we have participated to several Pasteur Courses (Molecular and Cellular Genetics, Mouse Molecular Genetics, Proteins Biochemistry) and to the FEBS course on Human and Microbial Genomics (Athens, March 30th - April 7th, 2006).

The PF also exerts a bibliographical and technical survey activity (wet and dry lab) so to rapidly integrate all the technological improvements and new applications of this technology.

  Web Site

More informations on our web site


Publications 2006 of the unit on Pasteur's references database

Activity Reports 2006 - Institut Pasteur
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