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PMID: 18631455 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

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

Immunity ·Vol. 29 ·No. 1 ·2008-07-18 ·Pages 150-64

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

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.

MeSH Terms
Adolescent Child Computational Biology/methods Disease Progression Female Gene Expression Profiling/methods Genomics/methods Humans Lupus Erythematosus, Systemic/blood,genetics Male Oligonucleotide Array Sequence Analysis/methods
Authors & Affiliations
29 authors, click to expand affiliations / ORCID
Chaussabel Damien
Baylor NIAID Cooperative Center for Translational Research on Human Immunology and Biodefense, Baylor Institute for Immunology Research and Baylor Research Institute, Dallas, TX 75204, USA. damienc@baylorhealth.edu
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
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Article Info
Journal
Immunity
Abbr.
Immunity
ISSN
1097-4180
DOI
10.1016/j.immuni.2008.05.012
Email
damienc@baylorhealth.edu
Published
2008-07-18
Pages
150-64
Language
English
Region
United States
NLM ID
9432918
PMCID
PMC2727981
Subset
IM
Grants
NIAID NIH HHS · U19 AI057234-04 · United States
NCI NIH HHS · R01 CA078846-07 · United States
NCI NIH HHS · R01 CA078846-02 · United States
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NIAMS NIH HHS · P50 AR054083-020001 · United States
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NCI NIH HHS · R01 CA078846-04 · United States
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NIAID NIH HHS · R01 AI068842-02 · United States
NCI NIH HHS · P01 CA084512-06 · United States
NIAMS NIH HHS · R01 AR050770 · United States
NCI NIH HHS · R01 CA078846-06 · United States
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NIAID NIH HHS · U19 AI057234-03 · United States
PHS HHS · R01 I068842 · United States
NCI NIH HHS · R01 CA078846-03 · United States
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NIAID NIH HHS · U19 AI057234-05S10013 · United States
PHS HHS · U19 AIO57234-02 · United States
NIAMS NIH HHS · P50 AR054083 · United States
NIAMS NIH HHS · P50 AR054083-02 · United States
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NCI NIH HHS · P01 CA084512-07 · United States
NCI NIH HHS · P01 CA084512-040003 · United States
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Databases
GEO
GSE11907
Corrections
CommentIn
PMID: 18631452
External Links
PubMed source DOI: 10.1016/j.immuni.2008.05.012 PMC Full Text View journal details
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