Integration of the GeneAtlasTM System
in a full experimental/analytical process
at BIOalternatives .
Analysis of genome-wide mRNA profiles.

BIOalternatives offers the largest panel of models and methods for cellular and molecular pharmacology. Our strength is to manage all the steps of a study process, from biological testing to data interpretation. We now offer the latest analytical technology through full human transcriptome profiling using the GeneAtlasTM system microarray platform and associated tools and software. It is now possible to generate global information regarding gene expression in a specific model, but also

  • to predict the activity of new compounds,
  • to find new activities of compounds (repositioning),
  • to discover new targets from condition or compound testing,
  • to assess potential side-effects (safety),
  • to analyse clinical samples as well as in vitro/ex vivo samples.

This highly indicative technology is also highly "sensitive" and needs a dedicated environment and expertise for its optimal management.



Cell & tissue sample preparation

  • Basal models (in vitro 2D, 3D, ex vivo),
  • Modified or not (stressed, aged...)
  • Testing of compounds,
  • Clinical samples.


RNA extraction, labeling process & quality control



Hybridization on Human Genome U219 array


The GeneAtlasTM system is a complete personal microarray solution for processing Affymetrix expression arrays. The HG U219 array is proposed for cosmetics purposes.


LIMS centralization


All the raw data are transferred and secured into BIOalternatives' LIMS, allowing the convenient recovery of the data and the profiling of selected genes in the different samples.




Excel file generation, LIMS transfer


Raw data reduction provides randomized relative expression values for each gene probe set and for each analyzed sample. Average replicate data (n=3 recommended for a single comparison) are analyzed in terms of statistical significance (p value) and a comprehensive Excel file (49386 lines) is generated for each comparison allowing the identification/selection of potentially modulated probe sets/genes.


Basic data analysis


From the basic Excel file, overall comparison tables are provided (number of potentially modulated probesets...) and illustrations (scatterplots) that show the overall difference level between the two compared samples.



Basic biological process analysis (computer-assisted clustering)


Modulated genes can be first grouped regarding their implication in biological pathways using the Ariadne Pathway Studio software. From this basic biological analysis it is possible to identify potential pathways, families of target genes and define an overall effect and potential claims.


Advanced analysis


An advanced computer-assisted biological analysis can be performed a second time, allowing more in-depth comprehension of the pathways involved or in the families of genes that are modulated in the different conditions. Finally, a gene per gene analysis of the results is performed even if these approaches are time-consuming and dependent on the number of genes/pathways that are modulated.



Full transcriptome analysis is a wonderful tool for molecular pharmacology and allows many applications in testing. It generates full gene expression profiles and a lot of information that should be correctly processed and analyzed. The Affymetrix GeneAtlasTM system coupled to the new Human Genome U219 array represents a great advance in terms of accessibility to this technique. However, this is a sensitive technology and some rules have to be taken into account: 1) a good experimental design (replicate samples, kinetics of analysis…) and 2) a correct/rigorous interpretation of the results. That is to say that studies using this technology should be done in a dedicated/validated environment such as that proposed by BIOalternatives . As shown in the experimental and analytical workflow, the technology is also complex and should be reserved to high value studies or compounds, e.g. compounds of high interest for which biological targets have to be defined. This technology is first of all indicative and the results have to be confirmed and validated using other methods before being used in claims. The results can be first confirmed at the mRNA level using RT-qPCR, but also at the protein level through multiple end-point analysis, e.g. immunolabeling-based studies, or using signal transduction or functional assays. BIOalternatives also provides these solutions allowing the time/cost-effective management of the overall sequence of your preclinical research.



BIOalternatives, 1 bis rue des plantes 86160 GENCAY - France Tel: +33 (0)549.36.11.37
Fax: +33 (0)549.53.10.29
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