An integrated approach to infer and model the gene network in early development of the cnidarian Nematostella vectensis

Abstract:
We have developed new methods to analyze spatio-temporal gene expression patterns (in situ hybridizations) and morphological data (based on confocal light microscopy images) of Nematostella during early embryonic development. The gene expression images are processed with two-dimensional geometry extraction methods and cell-layer decomposition methods to consistently compare and model the expression patterns. Moreover, a three-dimensional tool has been developed for geometry extraction and decomposition of expression patterns that are not radially symmetric about the main body axis. The model parameters and gene network are inferred from the expression data using an optimization algorithm that is adapted to handle the relatively small amount of non-systematic measurements and to include biochemical knowledge from literature.