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; Marilynn Punaro; Knut M. Wittkowski; Perrin White; Joseph Fay; Goran Klintmalm; Octavio Ramilo; A. Karolina Palucka; Jacques Banchereau; Virginia Pascual

doi:10.1016/j.immuni.2008.05.012

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 LanierMarilynn Punaro, Knut M. Wittkowski, Perrin White, Joseph Fay, Goran Klintmalm, Octavio Ramilo, A. Karolina Palucka, Jacques Banchereau, Virginia Pascual

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521 Scopus citations

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 language	English (US)
Pages (from-to)	150-164
Number of pages	15
Journal	Immunity
Volume	29
Issue number	1
DOIs	https://doi.org/10.1016/j.immuni.2008.05.012
State	Published - Jul 18 2008

ASJC Scopus subject areas

Immunology and Allergy
Immunology
Infectious Diseases

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10.1016/j.immuni.2008.05.012

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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., ... 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

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

@article{f20dc7a785864cbd8d7b5e6907645ef8,

title = "A Modular Analysis Framework for Blood Genomics Studies: Application to Systemic Lupus Erythematosus",

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.",

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 Wittkowski, {Knut M.} and Perrin White and Joseph Fay and Goran Klintmalm and Octavio Ramilo and Palucka, {A. Karolina} and Jacques Banchereau and Virginia Pascual",

note = "Funding Information: This research was supported by the Baylor Health Care System Foundation, the Alliance for Lupus Research (V.P.), the DANA foundation (A.K.P.), the Defense Advanced Research Planning Agency (J.B.), and the National Institutes of Health (U19 AIO57234-02, P01 CA084512, R01 CA078846, and R01 I068842 to J.B.; Center for Lupus Research P50 AR054083 and R01 AR050770-01 to V.P.). J.B. holds the W.W. Caruth, Jr. Chair in Organ Transplantation Immunology. A.K.P. holds the Michael A. Ramsay Chair for Cancer Immunology Research. J. B. is a shareholder of Illumina, Inc. ",

year = "2008",

month = jul,

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doi = "10.1016/j.immuni.2008.05.012",

language = "English (US)",

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T1 - A Modular Analysis Framework for Blood Genomics Studies

T2 - Application to Systemic Lupus Erythematosus

AU - Chaussabel, Damien

AU - Quinn, Charles

AU - Shen, Jing

AU - Patel, Pinakeen

AU - Glaser, Casey

AU - Baldwin, Nicole

AU - Stichweh, Dorothee

AU - Blankenship, Derek

AU - Li, Lei

AU - Munagala, Indira

AU - Bennett, Lynda

AU - Allantaz, Florence

AU - Mejias, Asuncion

AU - Ardura, Monica

AU - Kaizer, Ellen

AU - Monnet, Laurence

AU - Allman, Windy

AU - Randall, Henry

AU - Johnson, Diane

AU - Lanier, Aimee

AU - Punaro, Marilynn

AU - Wittkowski, Knut M.

AU - White, Perrin

AU - Fay, Joseph

AU - Klintmalm, Goran

AU - Ramilo, Octavio

AU - Palucka, A. Karolina

AU - Banchereau, Jacques

AU - Pascual, Virginia

N1 - Funding Information: This research was supported by the Baylor Health Care System Foundation, the Alliance for Lupus Research (V.P.), the DANA foundation (A.K.P.), the Defense Advanced Research Planning Agency (J.B.), and the National Institutes of Health (U19 AIO57234-02, P01 CA084512, R01 CA078846, and R01 I068842 to J.B.; Center for Lupus Research P50 AR054083 and R01 AR050770-01 to V.P.). J.B. holds the W.W. Caruth, Jr. Chair in Organ Transplantation Immunology. A.K.P. holds the Michael A. Ramsay Chair for Cancer Immunology Research. J. B. is a shareholder of Illumina, Inc.

PY - 2008/7/18

Y1 - 2008/7/18

N2 - 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.

AB - 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.

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SN - 1074-7613

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EP - 164

JO - Immunity

JF - Immunity

IS - 1

ER -

A Modular Analysis Framework for Blood Genomics Studies: Application to Systemic Lupus Erythematosus

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