A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus
By D. Chaussabel, Charlie Quinn, Jing Shen, Pinakeen Patel, C. Glaser, Nicole E. Baldwin, D. Stichweh, D. Blankenship, Lei Li, Indira D Munagala and 19 more. Immunity, 2008
645 citations recorded by the source corpus.
Summary The analysis of patient blood transcriptional profiles offers a means to investigate 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 datasets. Mapping changes in gene expression at the module-level generated disease-specific transcriptional fingerprints which 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.
Subfields: Immunology, Radiology, Nuclear Medicine and Imaging, Rheumatology
View Paper: https://www.semanticscholar.org/paper/b74f2fb7d9b47b03d458c996df765e034b603064
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Citations in the corpus
- The immune response in tuberculosis. (2013, methodology): “Using a statistical approach termed “analysis of significance” (79) and a modular data-mining strategy of the blood transcriptome (80), we were able to distinguish patients with active TB from those with streptococcal and staphylococcal infections and autoimmune diseases (72).”
- Personalized Immunomonitoring Uncovers Molecular Networks That Stratify Lupus Patients (2016, positive): “To functionally interpret these DETs, we conducted modular analysis (Chaussabel et al., 2008).”
- Rare and Common Variants: Twenty arguments (2011, background): “By contrast, various blood disorders have been shown to correlate with extreme values for the major vectors of modules of gene expressio”
- Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. (2010, background): “At any rate, WBCs are commonly used in the search for novel SLE targets and have provided specific signatures associated with SLE pathogenesis (Bennett et al. 2003; Chaussabel et al. 2008).”