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18

Transcriptomics and Proteomics

Fig. 18.1 The major parts of proteomics and their interrelationships, and their relation to pharma-

ceutical drugs

in turn determines protein binding, localization, and so forth. These are all crucial

aspects of the dynamical system that precedes the phenotype in the overall genotype

right arrow→phenotype transformation.

These modifications increase the potential repertoire of proteins expressible from

genes by typically one to two orders of magnitude (since many combinations are

possible) compared with the repertoire of genes. Notice that effecting these modifi-

cations requires enzymes; hence, the proteome is highly self-referential.

Although the number of different proteins therefore far exceeds the number of

genes, the actual number of proteins present in a cell at any one instant may well be

much smaller than the number of genes, since only a part of the possible repertoire

is likely to be expressed. Each cell type in an organism has a markedly different

proteome. The proteome for a given cell type is, moreover, likely to depend on its

environment; unlike the genome, therefore, which is relatively static, the proteome

can be highly dynamic.

Proteomics is sometimes defined so as to encompass what is otherwise called inter-

actomics: the study of the ensemble of molecular interactions, especially protein–

protein interactions, in a cell, including those that lead to the formation of more or

less long-lived multiprotein complexes. These aspects are covered in Chap. 23.

18.1

Transcriptomics

The goal of transcriptomics is to identify, quantify, and analyse the amounts of all the

mRNA in a cell. This is mainly done using microarrays (“gene chips”). The principle

of a microarray is to coat a flat surface with spots of DNA complementary to the

expressed mRNA, which is then captured because of the complementary base-pairing

(hybridization) between DNA and RNA (A–U, C–G, G–C, T–A) and identified. The

relationship of a microarray to a classical affinity assay resembles that of a massively

parallel processor to a classical linear processor, in which instructions are executed