ArticleBMC bioinformatics2010
An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Protein Subdomain Enrichment ofFrontiers in cardiovascular medicine · 2020Article
- Phenotypic and Genotypic Eligible Methods forFrontiers in microbiology · 2017Review
- A comparison of conventional methods for the quantification of bacterial cells after exposure to metal oxide nanoparticles.BMC microbiology · 2014Article
- Characterization of intracellular growth regulator icgR by utilizing transcriptomics to identify mediators of pathogenesis in Shigella flexneri.Infection and immunity · 2013Article
- Transcriptional modulation of enterotoxigenic Escherichia coli virulence genes in response to epithelial cell interactions.Infection and immunity · 2013Article
- One test microbial diagnostic microarray for identification of Mycoplasma mycoides subsp. mycoides and other Mycoplasma species.Molecular biotechnology · 2012Article
- Shigella flexneri effectors OspE1 and OspE2 mediate induced adherence to the colonic epithelium following bile salts exposure.Molecular microbiology · 2012Article
- Prediction system for rapid identification of Salmonella serotypes based on pulsed-field gel electrophoresis fingerprints.Journal of clinical microbiology · 2012Article
- Analysis of global transcriptional profiles of enterotoxigenic Escherichia coli isolate E24377A.Infection and immunity · 2012Article
- Genomic characterization of enteroaggregative Escherichia coli from children in Mali.The Journal of infectious diseases · 2012Article
- Proceedings of the 2011 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. Introduction.BMC bioinformatics · 2011Article
- Molecular and comparative analysis of Salmonella enterica Senftenberg from humans and animals using PFGE, MLST and NARMS.BMC microbiology · 2011Article
- Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference.BMC bioinformatics · 2010Article
- ArrayTrack: a free FDA bioinformatics tool to support emerging biomedical research--an update.Human genomics · 2010Review
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Authors and funding
17 authors.
Funding
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Abstract
backgroundAdvances in microbial genomics and bioinformatics are offering greater insights into the emergence and spread of foodborne pathogens in outbreak scenarios. The Food and Drug Administration (FDA) has developed a genomics tool, ArrayTrack™, which provides extensive functionalities to manage, analyze, and interpret genomic data for mammalian species. ArrayTrack™ has been widely adopted by the research community and used for pharmacogenomics data review in the FDA's Voluntary Genomics Data Submission program.
resultsArrayTrack™ has been extended to manage and analyze genomics data from bacterial pathogens of human, animal, and food origin. It was populated with bioinformatics data from public databases such as NCBI, Swiss-Prot, KEGG Pathway, and Gene Ontology to facilitate pathogen detection and characterization. ArrayTrack™'s data processing and visualization tools were enhanced with analysis capabilities designed specifically for microbial genomics including flag-based hierarchical clustering analysis (HCA), flag concordance heat maps, and mixed scatter plots. These specific functionalities were evaluated on data generated from a custom Affymetrix array (FDA-ECSG) previously developed within the FDA. The FDA-ECSG array represents 32 complete genomes of Escherichia coli and Shigella. The new functions were also used to analyze microarray data focusing on antimicrobial resistance genes from Salmonella isolates in a poultry production environment using a universal antimicrobial resistance microarray developed by the United States Department of Agriculture (USDA).
conclusionThe application of ArrayTrack™ to different microarray platforms demonstrates its utility in microbial genomics research, and thus will improve the capabilities of the FDA to rapidly identify foodborne bacteria and their genetic traits (e.g., antimicrobial resistance, virulence, etc.) during outbreak investigations. ArrayTrack™ is free to use and available to public, private, and academic researchers at http://www.fda.gov/ArrayTrack.
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