Creation of a New Competence in Bio-Informatics and of a Technological Platform for Large-Scale Genome Analysis - DNA CHIPS

Coordinating Institution: CRP Sante
Contracting Partner(s): University of Luxembourg
Other Partner(s): Institut de Génétique et de Biologie Moléculaire, Strasbourg (F) , Laboratoire de Biochimie et de Biologie Moléculaire, Strasbourg (F)
From: 01/02/2002
To: 31/01/2009
Budget: 1,400,000.00€
Contact(s): Friederich Evelyne , Vallar Laurent

Summary

We previously designed and carefully benchmarked a thematic microarray called Actichip that showed robust performance as a tool to profile the expression level of about 2000 genes coding for key proteins from the actin cytoskeleton and associated regulatory pathways. Possible applications for this biochip are numerous, in particular in the field of oncology where it can be used to profile the changes in gene expression accompanying tumour progression and help identifying target genes for diagnostic, prognostic or therapeutic purpose.

During the last phase of the project, we used Actichip to analyse the transcriptome of various human normal and tumour specimens, as well as cell lines. We obtained high quality gene expression datasets that were further analysed using specific statistical methods, and we identified several groups of genes with significant expression patterns characteristic of each of the sample types that we tested. Based on a subset of these genes, we were able to discriminate normal and tumour samples and to correctly classify them into distinct histopathological subgroups. In addition to the initial work program, we also built a large gene expression database by retrieving, re-annotating, filtering and normalising data available in the public repositories GEO (NCBI) and ArrayExpress (EBI).

The database currently compiles high quality expression data from 90 microarray studies including 7381 experiments performed with human normal and tumour samples from 41 tissue categories using five microarray platforms. Through a meta-analysis of these data, we confirmed that a majority of the genes identified using Actichip has tissue- or cancer-specific expression pattern. The value of these genes as biomarkers should now be validated through the screening of representative panels of clinical samples.

Refereed Scientific Publications:
  • Janji B, Vallar L, Al-Tanoury Z, Bernardin F, Vetter G, Schaffner-Reckinger E, Berchem G, Friederich E, Chouaib S. Cell Mol Med, 2009 (In Press).
Other Publications
  • Loïc COUDERC « Méta-analyse de données d’expression génique relatives aux gènes du cytosquelette d’actine », Master thesis, Septembre 2009, Université de Bordeaux 1, France.
Project Websites: