The study of the transcriptome is rapidly advancing the biological knowledge of pathogenic organisms. Microarray technology allows us to identify, in a holistic manner, all of the components in an organism that work together to mediate their pathogenic activities [47, 48]. In particular, many new virulence factors have been identified without having to revert to the laborious techniques of the past . The true importance of transcriptomics and microarrays is probably best shown by the diverse range of areas in addition to pathogen transcriptomics to which microarrays are contributing significantly, including (among many others) operon identification , gene essentiality studies , genotyping , detection of virulent isolates , elucidation of the host response to infection , and the effect of virulent organisms on host cells .
Transcriptomics is used as an indication of cellular activity at the protein level. In prokaryotes there is thought to be a high (but not an absolute) correlation between transcription and translation. Although there will always be exceptions to this, studies have been performed that assessed the relationship between tran-scriptional activities and the resulting level of biological activity at the protein level . An obvious drawback becoming apparent to this kind of study is that the current technology available to analyze the proteome of a cell is far behind that used to analyze the transcriptome. For example, Scherl et al.  were able to identify proteins corresponding to just 23% of the Staphylococcus aureus predicted ORFs despite using a myriad of technologies to increase their detection rate. To fully unravel the story of a host and its pathogen, much more work is needed in exploring the integration of transcriptomic data with that derived from proteomic studies.
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