Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques

Sundaresh, Suman, Doolan, Denise L., Hirst, Siddiqua, Mu, Yunxiang, Unal, Berkay, Davies, D. Huw, Felgner, Philip L., and Baldi, Pierre (2006) Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques. Bioinformatics, 22 (14). pp. 1760-1766.

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Motivation: We present a study of antigen expression signals from a newly developed high-throughput protein microarray technique. These signals are a measure of antibody–antigen binding activity and provide a basis for understanding humoral immune responses to various infectious agents and supporting vaccine and diagnostic development.

Results: We investigate the characteristics of these expression profiles and show that noise models, normalization, variance estimation and differential expression analysis techniques developed in the context of DNA microarray analysis can be adapted and applied to these protein arrays. Using a high-dimensional dataset containing measurements of expression profiles of antibody reactivity against each protein (295 antigens and 9 controls) in 42 malaria (Plasmodium falciparum) protein arrays derived from 22 donors with various clinical presentations of malaria, we present a methodology for the analysis and identification of significantly expressed antigens targeted by immune responses for individual sera, groups of sera and across stages of infection. We also conduct a short study highlighting the top immunoreactive antigens where we identify three novel high priority antigens for future evaluation.

Item ID: 42749
Item Type: Article (Research - C1)
ISSN: 1367-4811
Funders: National Institutes of Health Bio-medical Informatics Training Program (NIHBITP), National Science Foundation (NSF), Institute for Genomics and Bioinformatics (IGB) (at University of California, Irvine), National Institute of Allergy and Infectious Diseases (NIAID)
Projects and Grants: NIHBITP Grant 5T15LM007743, NSF MRI EIA-0321390, NIAID Grant U01AI056464, NIAID Grant 1U01AI061363-01
Date Deposited: 21 Mar 2016 23:20
FoR Codes: 11 MEDICAL AND HEALTH SCIENCES > 1107 Immunology > 110799 Immunology not elsewhere classified @ 100%
SEO Codes: 92 HEALTH > 9201 Clinical Health (Organs, Diseases and Abnormal Conditions) > 920109 Infectious Diseases @ 100%
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