A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.


The analysis of patient blood transcriptional profiles offers a means to investigate the immunological mechanisms relevant to human diseases on a genome-wide scale. In addition, such studies provide a basis for the discovery of clinically relevant biomarker signatures. We designed a strategy for microarray analysis that is based on the identification of transcriptional modules formed by genes coordinately expressed in multiple disease data sets. Mapping changes in gene expression at the module level generated disease-specific transcriptional fingerprints that provide a stable framework for the visualization and functional interpretation of microarray data. These transcriptional modules were used as a basis for the selection of biomarkers and the development of a multivariate transcriptional indicator of disease progression in patients with systemic lupus erythematosus. Thus, this work describes the implementation and application of a methodology designed to support systems-scale analysis of the human immune system in translational research settings.

DOI: 10.1016/j.immuni.2008.05.012

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@article{Chaussabel2008AMA, title={A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.}, author={Damien Chaussabel and Charles Quinn and Jing Shen and Pinakeen Patel and Casey Glaser and Nicole Baldwin and Dorothee Stichweh and Derek Blankenship and Lei Li and Indira Munagala and Lynda Bennett and Florence Allantaz and Asuncion Mejias and Monica Ardura and Ellen Kaizer and Laurence Monnet and Windy Allman and Henry Randall and Diane Johnson and Aimee Lanier and Marilynn Punaro and Knut M Wittkowski and Perrin White and Joseph Fay and Goran Klintmalm and Octavio Ramilo and A Karolina Palucka and Jacques Banchereau and Virginia Pascual}, journal={Immunity}, year={2008}, volume={29 1}, pages={150-64} }