23.11 Metabolomics and Metabonomics

331

one that could be developed, with more sophistication, to extract interaction data

from sequence alone, which is a kind of Holy Graal for interactomics, since it is so

much easier nowadays to obtain sequence data than any other kind.

23.10 Global Statistics of Interactions

The experimental difficulties are still so onerous, the uncertainties so great, and the

amount of data is so little that researchers have mostly been content to draw diagrams,

essentially graphs, of their results, with the proteins as nodes and the associations

as vertices, and leave it at that; at most, a difference in the pattern between a pair of

sets of results from the same organism grown under two different conditions might

be attempted. An endeavour to go beyond this first stage of representation has been

made, ³⁵ with the result (from a single dataset covering protein–protein interactions

in yeast, with just under 1900 proteins and just over 2200 interactions) that the

probability that a given protein interacts with kk other proteins follows a power law

over about one and a half orders of magnitude with an exponenttilde negative 2∼−2. Unsurprisingly,

the most heavily connected proteins were also found to be the most likely to cause

lethality if knocked out.

23.11 Metabolomics and Metabonomics

Metabolism is the ensemble of chemical transformations carried out in living tissue

(Sect. 14.3); operationally it is embodied in the matter and energy fluxes through

organisms. Metabolomics is defined as the measurement of the amounts (concentra-

tions) and locations of all the metabolites in a cell, the metabolites being the small

molecules (upper M Subscript normal r Baseline less than or equivalent to 1000Mr ≲1000; e.g., glucose, cAMP, ³⁶ GMP, ³⁷ glutamate, etc.) transformed

in the process of metabolism (i.e., mostly the substrates and products of enzymes). ³⁸

The quantification of the amounts of expressed enzymes is, as we have seen, pro-

teomics; metabolomics is essentially an extension of proteomics to the activities of

35 Jeong et al. (2001).

36 Cyclic adenosine monophosphate.

37 Guanosine monophosphate.

38 The official classification of enzyme function is that of the Enzyme Commission (EC), which

recognizes six main classes: 1, oxidoreductases; 2, transferases; 3, hydrolases; 4, lyases; 5, iso-

merases; and 6, ligases. The main class number is followed by three further numbers (separated

by points), whose significance depends on the main class. For class 1, the second number denotes

the substrate and the third number denotes the acceptor; whereas for class 3, the second number

denotes the type of bond cleaved and the third number denotes the molecule in which that bond

is embedded. For all classes, the fourth number signifies some specific feature such as a particular

cofactor.