  Network motifs, the recurring regulatory structural patterns in networks, are
able to self-organize to produce networks. Three major motifs, feedforward
loop, single input modules and bi-fan are found in gene regulatory networks.
The large ratio of genes to transcription factors (TFs) in genomes leads to a
sharing of TFs by motifs and is sufficient to result in network
self-organization. We find a common design principle of these motifs: short
transcript's half-life (THL) TFs are significantly enriched in motifs and hubs.
This enrichment becomes one of the driving forces for the emergence of the
network scale-free topology and allows the network to quickly adapt to
environmental changes. Most feedforward loops and bi-fans contain at least one
short THL TF, which can be seen as a criterion for self-assembling these
motifs. We have classified the motifs according to their short THL TF content.
We show that the percentage of the different motif subtypes varies in different
cellular conditions.
