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A Modular Analysis Framework for Blood Genomics Studies: Application to Systemic Lupus Erythematosus
Open accessAbstract
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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“By contrast, various blood disorders have been shown to correlate with extreme values for the major vectors of modules of gene expression92.”
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Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., et al. (1999) · Science · doi:10.1126/science.286.5439.531 · Cited by 11,516
Harary, F. (1969) · Cited by 10,739
Mootha, V. K., Lindgren, C. M., Eriksson, K.-F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstråle, M., Laurila, E., et al. (2003) · Nature Genetics · doi:10.1038/ng1180 · Cited by 10,197
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling
Alizadeh, A. A., Eisen, M. B., Davis, R. E., Ma, C., Lossos, I. S., Rosenwald, A., Boldrick, J. C., Sabet, H., Tran, T., Yu, X., et al. (2000) · Nature · doi:10.1038/35000501 · Cited by 9,925
Fitzmaurice, G. M., Laird, N. M., & Ware, J. H. (2011) · Wiley Series in Probability and Statistics · doi:10.1002/9781119513469 · Cited by 4,639
Derivation of the sledai. A disease activity index for lupus patients
Bombardier, C., Gladman, D. D., Urowitz, M. B., Caron, D., Chang, C. H., Austin, A., Bell, A., Bloch, D. A., Corey, P. N., Decker, J. L., et al. (1992) · Arthritis & Rheumatism · doi:10.1002/art.1780350606 · Cited by 4,570
Linear Mixed Models for Longitudinal Data
Verbeke, G. (1997) · Lecture Notes in Statistics · doi:10.1007/978-1-4612-2294-1_3 · Cited by 3,506
Baechler, E. C., Batliwalla, F., Karypis, G., Gaffney, P. M., Ortmann, W. A., Espe, K. J., Shark, K. B., Grande, W. J., Hughes, K. M. H., Kapur, V., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0337679100 · Cited by 2,246
MAQC Consortium, Shi, L., Shi, L., Reid, L. H., Jones, W. D., Shippy, R., Warrington, J. A., Baker, S. C., Collins, P. J., de Longueville, F., et al. (2006) · Nature Biotechnology · doi:10.1038/nbt1239 · Cited by 2,126
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Bennett, L. B., Palucka, K., Arce, E., Cantrell, V., Borvák, J., Banchereau, J., & Pascual, V. (2003) · The Journal of Experimental Medicine · doi:10.1084/jem.20021553 · Cited by 1,990
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Metadata
- 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
- Venue
- Immunity
- Publisher
- Elsevier BV
- Published
- 2008-07
- Volume
- 29
- Issue
- 1
- Pages
- 150-164
- ISSN
- 1074-7613 (ISSN-L)
- 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
- 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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