Systems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targets

dc.contributor.authorMcGarvey, Peter B.en
dc.contributor.authorHuang, Hongzhanen
dc.contributor.authorMazumder, Rajaen
dc.contributor.authorZhang, Jianen
dc.contributor.authorChen, Yongxingen
dc.contributor.authorZhang, Chengdongen
dc.contributor.authorCammer, Stephenen
dc.contributor.authorWill, Rebeccaen
dc.contributor.authorOdle, Margieen
dc.contributor.authorSobral, Brunoen
dc.contributor.authorMoore, Margareten
dc.contributor.authorWu, Cathy H.en
dc.description.abstractThe NIAID (National Institute for Allergy and Infectious Diseases) Biodefense Proteomics program aims to identify targets for potential vaccines, therapeutics, and diagnostics for agents of concern in bioterrorism, including bacterial, parasitic, and viral pathogens. The program includes seven Proteomics Research Centers, generating diverse types of pathogen-host data, including mass spectrometry, microarray transcriptional profiles, protein interactions, protein structures and biological reagents. The Biodefense Resource Center ( has developed a bioinformatics framework, employing a protein-centric approach to integrate and support mining and analysis of the large and heterogeneous data. Underlying this approach is a data warehouse with comprehensive protein + gene identifier and name mappings and annotations extracted from over 100 molecular databases. Value-added annotations are provided for key proteins from experimental findings using controlled vocabulary. The availability of pathogen and host omics data in an integrated framework allows global analysis of the data and comparisons across different experiments and organisms, as illustrated in several case studies presented here. (1) The identification of a hypothetical protein with differential gene and protein expressions in two host systems (mouse macrophage and human HeLa cells) infected by different bacterial (Bacillus anthracis and Salmonella typhimurium) and viral (orthopox) pathogens suggesting that this protein can be prioritized for additional analysis and functional characterization. (2) The analysis of a vaccinia-human protein interaction network supplemented with protein accumulation levels led to the identification of human Keratin, type II cytoskeletal 4 protein as a potential therapeutic target. (3) Comparison of complete genomes from pathogenic variants coupled with experimental information on complete proteomes allowed the identification and prioritization of ten potential diagnostic targets from Bacillus anthracis. The integrative analysis across data sets from multiple centers can reveal potential functional significance and hidden relationships between pathogen and host proteins, thereby providing a systems approach to basic understanding of pathogenicity and target identification.en
dc.description.sponsorshipSupported by National Institutes of Allergy and Infectious Disease NIH Contract: HHSN266200400061C The funders had no role in study design, analysis, decision to publish, or preparation of the manuscript. The funders, NIAID, did play some role in data collection as they had contracts with the Proteomics Research Centers that provided the data. The contracts provided guidelines on data collection and submission to the Resource Center and require release to the public. Social and Scientific Systems is an IT contractor and has no interest, finacial or otherwise, in the data, software or conclusions in this manuscripten
dc.identifier.citationMcGarvey PB, Huang H, Mazumder R, et al. Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets. PLoS One. 2009;4:e7162.
dc.publisherPublic Library of Scienceen
dc.rightsIn Copyrighten
dc.subjectMass spectrometryen
dc.subjectMicroarray transcriptional profilesen
dc.subjectProtein interactionsen
dc.titleSystems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targetsen
dc.title.serialPLoS ONEen
dc.typeArticle - Refereeden


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