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Computational Systems Neurobiology pp 1–22Cite as

Functional Genomics and Molecular Networks Gene Expression Regulations in Complex Diseases: Down Syndrome as a Case Study

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Abstract

The goal of functional genomics is to understand the relationship between whole genomes and phenotypes through a dynamic approach. It requires high throughput technologies such as microarrays and data analysis. The power of this approach allowed to study complex biological functions as well as diseases. In this chapter, we introduce functional genomics and describe the statistical methods that are used to find differentially expressed genes. We analyze a large number of data sets produced on a complex disease, namely Down syndrome, in different models. We show that, whatever the model, genes that are in three copies are globally overexpressed. However, we failed to identify a set of two-copy genes that would be dysregulated in all studies. It either suggests that studies are incomplete, or that this set of genes does not exist and that overexpression of the three-copy genes impacts on the whole transcriptome in a “stochastic” way.

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Notes

  1. 1.

    Transforming expression data to a log scale (any base) reduces the asymmetry of the distribution of the intensities and homogenizes their variance. Here, probe intensities are systematically log2values.

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Acknowledgements

The authors wish to thank The European program AnEUploidy and the Fondation Jérôme Lejeune for their financial support.

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Authors and Affiliations

  1. CRICM, CNRS UMR7225, INSERM U975 and UPMC, Hôpital de la Pitié-Salpêtrière, 47 Bd de l’Hôpital, ICM, Room 5.041, 75013, Paris, France

    Marie-Claude Potier

  2. ESA, ESPCI ParisTech, 10 rue Vauquelin, 75005, Paris, France

    Isabelle Rivals

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  1. Marie-Claude Potier
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  2. Isabelle Rivals
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Correspondence to Marie-Claude Potier .

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Editors and Affiliations

  1. European Bioinformatics Institute, EMBL-Outstation-Hinxton, Wellcome Trust Genome Campus, Welcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom

    N. Le Novère

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Potier, MC., Rivals, I. (2012). Functional Genomics and Molecular Networks Gene Expression Regulations in Complex Diseases: Down Syndrome as a Case Study. In: Le Novère, N. (eds) Computational Systems Neurobiology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-3858-4_1

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