%0 Journal Article
%T Inferring Drosophila gap gene regulatory network: pattern analysis of simulated gene expression profiles and stability analysis
%A Yves Fomekong-Nanfack
%A Marten Postma
%A Jaap A Kaandorp
%J BMC Research Notes
%D 2009
%I BioMed Central
%R 10.1186/1756-0500-2-256
%X We have analyzed the simulated gene expression patterns of previously obtained circuits that describe gap gene dynamics during early Drosophila melanogaster embryogenesis. Using hierarchical clustering we show that amplitude variation and defects observed in the simulated gene expression patterns are linked to similar circuits, which can be grouped. Furthermore, analysis of the long-term dynamics revealed four main dynamical attractors comprising stable patterns and oscillatory patterns. In addition, we also performed a correlation analysis on the parameters showing an intricate correlation pattern.The analysis demonstrates that the obtained gap gene circuits are not unique showing variable long-term dynamics and highly correlating scattered parameters. Furthermore, although the model can simulate the pattern up to gastrulation and confirms several of the known regulatory interactions, it does not reproduce the transient expression of all gap genes as observed experimentally. We suggest that the shortcomings of the model may be caused by overfitting, incomplete model description and/or missing data.A biological system that has been extensively studied is the segmentation mechanism of early development in Drosophila melanogaster (see [1] for review). At early stage, a cascade of maternal and zygotic genes is activated in the syncytial embryo that subdivides the ectoderm into smaller domains. First, maternal morphogenes such as bicoid (bcd), caudal (cad) and hunchback (hb) activate zygotic gap genes such as hb, giant (gt), Kr¨ąppel (Kr), knirps (kni), or tailles (tll), which in turn will activate the pair rule genes. The pair rule genes will regulate segment polarity genes and Hox genes, which both control the differentiation of each segment of the future embryo [1].The gap gene circuit has been extensively investigated using mathematical models [2,3]. In all cases, the goal was to derive the regulatory interactions that control gene expression. The gene circuit approa
%U http://www.biomedcentral.com/1756-0500/2/256