Transcriptomics 8/1/03. By Richard Twyman The global study of gene expression at the RNA level.

The human genome contains the complete set of genes required to build a functional human being. However, the genome is only a source of information. In order to function, it must be expressed. The transcription of genes to produce RNA is the first stage of gene expression . The transcriptome is the complete set of RNA transcripts produced by the genome at any one time.

Unlike the genome, the transcriptome is extremely dynamic. Most of our cells contain the same genome regardless of the type of cell, stage of development or environmental conditions. Conversely, the transcriptome varies considerably in these differing circumstances due to different patterns of gene expression. Transcriptomics, the study of the transcriptome, is therefore a global way of looking at gene expression patterns.

Why is transcriptomics of interest? There are many different ways in which the large-scale analysis of gene expression patterns can be useful. These include:

• To answer specific questions about gene expression. For example, which genes are activated by a particular transcription factor? This sort of question can be addressed by comparing gene expression patterns in tissues in which the particular transcription factor is either active or inactive.
• General discovery experiments. These have no particular hypothesis but can be used to identify interesting genes. For example, which genes are highly expressed in brain tumours but not in healthy brain tissue? Can these be used as drug targets or diagnostic markers?
• Disease classification. Sometimes single markers are not sufficient to distinguish two similar diseases, as is often the case in cancer. Testing the expression profiles of a larger number of genes can provide accurate diagnoses.
• Functional annotation. Many DNA sequences that have been isolated have no known function. However, if they show similar expression patterns to a characterised gene, it is likely their functions are similar. It is sometimes possible to identify conserved regulatory elements in such genes.
• To identify drug targets. If the gene expression profile caused by a mutation is similar to that caused by a drug, it is likely the drug interacts with and inactivates the protein affected by the mutation.
• How is transcriptomics studied? There are a number of different methods but currently the most popular is the use of DNA microarrays .

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