Estimating optimal sparseness of developmental gene networks using a semi-quantitative model

<div><p>To estimate gene regulatory networks, it is important that we know the number of connections, or sparseness of the networks. It can be expected that the robustness to perturbations is one of the factors determining the sparseness. We reconstruct a semi-quantitative model of gene networks from gene expression data in embryonic development and detect the optimal sparseness against perturbations. The dense networks are robust to connection-removal perturbation, whereas the sparse networks are robust to misexpression perturbation. We show that there is an optimal sparseness that serves as a trade-off between these perturbations, in agreement with the optimal result of validation for testing data. These results suggest that the robustness to the two types of perturbations determines the sparseness of gene networks.</p></div

MOESM3 of The role of retinoic acid signaling in starfish metamorphosis

Additional file 3: Table S1. Accession numbers of the gene used for construction of phylogenic tree. Amino acid sequences to construct tree were obtained from Uniprot or Echinobase ( http://www.echinobase.org/Echinobase/ ), Genbank