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a) b) c) d) e) f )
Fig. 2.4. Network motifs, examples [93]: a { the feedforward loop, b { three nodes chain, c -
bi-parallel, d { three nodes feedback loop, e { four nodes feedback loop, f { bi-fan. The dierent
motifs are dierentially enriched in dierent networks, suggesting the use of dierent building
blocks for networks with dierent purposes, see text for details.
reect the underlying processes that generated each type of network; for example,
food webs evolve to allow a ow of energy from the bottom to the top of food
chains, whereas gene regulation and neuron networks evolve to process information.
Information processing seems to give rise to signicantly dierent structures than
does energy ow.
2.8. Conclusion
Biological research in the past focused on single gene/protein - analysis so that
for a small fraction of all known genes/proteins there is a lot of information avail-
able. However, it is today clear that many biological processes cannot be studied
with such a reductionistic approach. Protein and DNA interact at the level of pro-
moters to nely tune gene expression; this is mainly accomplished in response to
specic environmental conditions that are integrated in cell behavior through in-
teraction networks composed by signal transduction cascades. In some sense the
environmental information ows through dierent biological networks to elicit a
specic response. One meaningful way to study the properties of these intricate
relationships is in the framework of network theory which allows the qualitative
and quantitative characterization of the most important features of a network by
means of well-dened statistics. In the last years, the availability of techniques for
high throughput analysis in biology enormously boosted such approach which also
took advantage of the development of computational methods that today represent
essential components of biological research; the challenge of systems biology is to
integrate the dierent -omics to fully elucidate the functioning of living cells and
progressing to eective medicine therapies.
