  Genes are frequently regulated in complex manners, necessitating modelling
approaches which go beyond simple (linear) gene-to-gene interactions and
address the modularity of cis-regulatory regions and alternate transcription
initiation sites. In particular, sharp expression patterns (peaks or stripes)
indicate that gene regulation involves nonlinear transcription factor kinetics
(beyond first-order). We propose a methodology for approaching this problem,
using the example of the multiple cis-regulatory modules (CRMs) and two
transcripts (P1 and P2) found in the Drosophila hunchback (hb) and (CD1 and
CD2)in Kruppel (Kr) genes, the genes expressed along the anteroposterior axis
of the embryo. The positional characteristics of the mRNA expression patterns
are studied for their sensitivity to the variation of the input factors and
initial conditions.
