The blood transcriptome affords a comprehensive view of the status of the human immune system. Global changes in transcript abundance have been measured in the blood of patients with a wide range of diseases. This chapter presents an overview of the advances that have led to the identification of therapeutic targets and biomarker signatures in the field of autoimmunity and infectious disease. It also provides technology and data analysis primers as means of introducing blood transcriptome research to a broad readership. Specifically, we compare microarrays with some of the most recent digital gene expression profiling technologies available to date, including RNA sequencing. Furthermore, in addition to the basic steps involved in the analysis of microarray data we also present more advanced data mining approaches for blood transcriptional fingerprinting.
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