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Open AccessArticle

The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis

1
Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
2
Epigenetics & Functional Genomics Laboratories, Department of Research and Development, Bay Pines Veteran Administration Healthcare System, Bay Pines, FL 33744, USA
*
Author to whom correspondence should be addressed.
J. Pers. Med. 2019, 9(2), 21; https://doi.org/10.3390/jpm9020021
Received: 30 March 2019 / Revised: 20 April 2019 / Accepted: 25 April 2019 / Published: 29 April 2019
(This article belongs to the Special Issue Personalized and Targeted Atherosclerosis Treatments)
As one of the most widespread metabolic diseases, atherosclerosis affects nearly everyone as they age; arteries gradually narrow from plaque accumulation over time reducing oxygenated blood flow to central and periphery causing heart disease, stroke, kidney problems, and even pulmonary disease. Personalized medicine promises to bring treatments based on individual genome sequencing that precisely target the molecular pathways underlying atherosclerosis and its symptoms, but to date only a few genotypes have been identified. A promising alternative to this genetic approach is the identification of pathways altered in atherosclerosis by transcriptome analysis of atherosclerotic tissues to target specific aspects of disease. Transcriptomics is a potentially useful tool for both diagnostics and discovery science, exposing novel cellular and molecular mechanisms in clinical and translational models, and depending on experimental design to identify and test novel therapeutics. The cost and time required for transcriptome analysis has been greatly reduced by the development of next generation sequencing. The goal of this resource article is to provide background and a guide to appropriate technologies and downstream analyses in transcriptomics experiments generating ever-increasing amounts of gene expression data. View Full-Text
Keywords: atherosclerosis; coronary aortic disease; gene set enrichment analysis; heart disease; metabolic disease; transcriptomics; pathway enrichment analysis; RNA-seq analysis; secondary gene expression analysis atherosclerosis; coronary aortic disease; gene set enrichment analysis; heart disease; metabolic disease; transcriptomics; pathway enrichment analysis; RNA-seq analysis; secondary gene expression analysis
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MDPI and ACS Style

Marín de Evsikova, C.; Raplee, I.D.; Lockhart, J.; Jaimes, G.; Evsikov, A.V. The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis. J. Pers. Med. 2019, 9, 21.

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