A Modular Analysis Framework for Blood Genomics Studies

Application to Systemic Lupus Erythematosus

Damien Chaussabel, Charles Quinn, Jing Shen, Pinakeen Patel, Casey Glaser, Nicole Baldwin, Dorothee Stichweh, Derek Blankenship, Lei Li, Indira Munagala, Lynda Bennett, Florence Allantaz, Asuncion Mejias, Monica Ardura, Ellen Kaizer, Laurence Monnet, Windy Allman, Henry Randall, Diane Johnson, Aimee Lanier & 9 others Marilynn Punaro, Knut M. Wittkowski, Perrin White, Joseph Fay, Goran Klintmalm, Octavio Ramilo, A. Karolina Palucka, Jacques Banchereau, Virginia Pascual

Research output: Contribution to journalArticle

375 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)150-164
Number of pages15
JournalImmunity
Volume29
Issue number1
DOIs
StatePublished - Jul 18 2008

Fingerprint

Genomics
Systemic Lupus Erythematosus
Biomarkers
Translational Medical Research
Gene Regulatory Networks
Dermatoglyphics
Microarray Analysis
Disease Progression
Immune System
Genome
Gene Expression

ASJC Scopus subject areas

  • Immunology and Allergy
  • Infectious Diseases
  • Immunology

Cite this

Chaussabel, D., Quinn, C., Shen, J., Patel, P., Glaser, C., Baldwin, N., ... Pascual, V. (2008). A Modular Analysis Framework for Blood Genomics Studies: Application to Systemic Lupus Erythematosus. Immunity, 29(1), 150-164. https://doi.org/10.1016/j.immuni.2008.05.012

A Modular Analysis Framework for Blood Genomics Studies : Application to Systemic Lupus Erythematosus. / Chaussabel, Damien; Quinn, Charles; Shen, Jing; Patel, Pinakeen; Glaser, Casey; Baldwin, Nicole; Stichweh, Dorothee; Blankenship, Derek; Li, Lei; Munagala, Indira; Bennett, Lynda; Allantaz, Florence; Mejias, Asuncion; Ardura, Monica; Kaizer, Ellen; Monnet, Laurence; Allman, Windy; Randall, Henry; Johnson, Diane; Lanier, Aimee; Punaro, Marilynn; Wittkowski, Knut M.; White, Perrin; Fay, Joseph; Klintmalm, Goran; Ramilo, Octavio; Palucka, A. Karolina; Banchereau, Jacques; Pascual, Virginia.

In: Immunity, Vol. 29, No. 1, 18.07.2008, p. 150-164.

Research output: Contribution to journalArticle

Chaussabel, D, Quinn, C, Shen, J, Patel, P, Glaser, C, Baldwin, N, Stichweh, D, Blankenship, D, Li, L, Munagala, I, Bennett, L, Allantaz, F, Mejias, A, Ardura, M, Kaizer, E, Monnet, L, Allman, W, Randall, H, Johnson, D, Lanier, A, Punaro, M, Wittkowski, KM, White, P, Fay, J, Klintmalm, G, Ramilo, O, Palucka, AK, Banchereau, J & Pascual, V 2008, 'A Modular Analysis Framework for Blood Genomics Studies: Application to Systemic Lupus Erythematosus', Immunity, vol. 29, no. 1, pp. 150-164. https://doi.org/10.1016/j.immuni.2008.05.012
Chaussabel, Damien ; Quinn, Charles ; Shen, Jing ; Patel, Pinakeen ; Glaser, Casey ; Baldwin, Nicole ; Stichweh, Dorothee ; Blankenship, Derek ; Li, Lei ; Munagala, Indira ; Bennett, Lynda ; Allantaz, Florence ; Mejias, Asuncion ; Ardura, Monica ; Kaizer, Ellen ; Monnet, Laurence ; Allman, Windy ; Randall, Henry ; Johnson, Diane ; Lanier, Aimee ; Punaro, Marilynn ; Wittkowski, Knut M. ; White, Perrin ; Fay, Joseph ; Klintmalm, Goran ; Ramilo, Octavio ; Palucka, A. Karolina ; Banchereau, Jacques ; Pascual, Virginia. / A Modular Analysis Framework for Blood Genomics Studies : Application to Systemic Lupus Erythematosus. In: Immunity. 2008 ; Vol. 29, No. 1. pp. 150-164.
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