Cited by 655Gene expression and cancer classificationSystemic Lupus Erythematosus ResearchBioinformatics and Genomic Networks

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

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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·2008·Immunity

DOI 10.1016/j.immuni.2008.05.012PMC PMC2727981

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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.

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Authors: 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, K. M., White, P., Fay, J., Klintmalm, G., Ramilo, O., Palucka, A. K., Banchereau, J., & Pascual, V.
Affiliations: National Institute of Allergy and Infectious Diseases (US)
Baylor University (US)
Baylor Scott & White Health (US)
Children's Medical Center (US)
Rockefeller University (US)
Corresponding author: Chaussabel, Damien
Banchereau, Jacques
ORCID: Chaussabel, Damien
Quinn, Charles
Shen, Jing
Baldwin, Nicole
Li, Lei
Bennett, Lynda
Ardura, Monica
Randall, Henry
Wittkowski, Knut M.
White, Perrin
Ramilo, Octavio
Banchereau, Jacques
Pascual, Virginia
Venue: Immunity
Publisher: Elsevier BV
Published: 2008-07
Volume: 29
Issue: 1
Pages: 150-164
ISSN: 1074-7613 (ISSN-L)
DOI: 10.1016/j.immuni.2008.05.012
PMC: PMC2727981
OpenAlex: W2150932450
Cited by: 649
References: 49
Citations by year: 2026: 21 · 2025: 18 · 2024: 25 · 2023: 30 · 2022: 26 · 2021: 50 · 2020: 40 · 2019: 42 · 2018: 42 · 2017: 32 · 2016: 46 · 2015: 47 · 2014: 37 · 2013: 52 · 2012: 41
FWCI: 13.70
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 1878 d)
Locations: Immunity (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: U.S. Public Health Service (U19 AIO57234-02, R01 I068842)
National Cancer Institute (P01CA084512, R01CA078846)
National Institute of Allergy and Infectious Diseases (U19AI057234, R01AI068842)
National Institute of Arthritis and Musculoskeletal and Skin Diseases (R01AR050770, P50AR055503, P50AR054083)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
Health Sciences › Medicine › Rheumatology › Systemic Lupus Erythematosus Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords: systemic lupus erythematosus, transcriptional modules, gene expression profiling, microarray data analysis, biomarker discovery, immune system, blood transcriptome
MeSH terms: Adolescent, Child, Female, Humans, Lupus Erythematosus, Systemic, Male, Disease Progression, Computational Biology, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Genomics

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

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