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Open Access Highly Accessed Methodology article

Simultaneous analysis of distinct Omics data sets with integration of biological knowledge: Multiple Factor Analysis approach

Marie de Tayrac12, Sébastien Lê3*, Marc Aubry4, Jean Mosser124* and François Husson3

Author Affiliations

1 CNRS UMR 6061, Université de Rennes 1, IFR 140, Faculté de Médecine, CS 34317, 35043 Rennes, France

2 Medical genomics Unit, Department of Biochemistry and molecular genetics, CHU Rennes, France

3 CNRS UMR 6625, Laboratoire de mathématiques appliquées, Agrocampus Rennes, France

4 Transcriptomic platform, Ouest-Genopole®, IFR 140, Rennes, France

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BMC Genomics 2009, 10:32  doi:10.1186/1471-2164-10-32

Published: 20 January 2009

Abstract

Background

Genomic analysis will greatly benefit from considering in a global way various sources of molecular data with the related biological knowledge. It is thus of great importance to provide useful integrative approaches dedicated to ease the interpretation of microarray data.

Results

Here, we introduce a data-mining approach, Multiple Factor Analysis (MFA), to combine multiple data sets and to add formalized knowledge. MFA is used to jointly analyse the structure emerging from genomic and transcriptomic data sets. The common structures are underlined and graphical outputs are provided such that biological meaning becomes easily retrievable. Gene Ontology terms are used to build gene modules that are superimposed on the experimentally interpreted plots. Functional interpretations are then supported by a step-by-step sequence of graphical representations.

Conclusion

When applied to genomic and transcriptomic data and associated Gene Ontology annotations, our method prioritize the biological processes linked to the experimental settings. Furthermore, it reduces the time and effort to analyze large amounts of 'Omics' data.