ArticleBMC systems biology2012
Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster.
Article in BMC systems biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Recovering time-varying networks from single-cell data.Bioinformatics (Oxford, England) · 2025Article
- Combined topological and spatial constraints are required to capture the structure of neural connectomes.Network neuroscience (Cambridge, Mass.) · 2025Article
- Studying temporal dynamics of single cells: expression, lineage and regulatory networks.Biophysical reviews · 2024Review
- Mean residence times of TF-TF and TF-miRNA toggle switches.Journal of biosciences · 2022Article
- The developmental-genetics of canalization.Seminars in cell & developmental biology · 2019Review
- Article
- A gene regulatory program controlling early Xenopus mesendoderm formation: Network conservation and motifs.Seminars in cell & developmental biology · 2017Review
- A TORC2-Akt Feed-Forward Topology Underlies HER3 Resiliency in HER2-Amplified Cancers.Molecular cancer therapeutics · 2015Article
- Design principles of stripe-forming motifs: the role of positive feedback.Scientific reports · 2014Article
- Transduction motif analysis of gastric cancer based on a human signaling network.Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologica · 2014Article
- Dynamics and precision in retinoic acid morphogen gradients.Current opinion in genetics & development · 2012Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNetwork motifs provided a "conceptual tool" for understanding the functional principles of biological networks, but such motifs have primarily been used to consider static network structures. Static networks, however, cannot be used to reveal time- and region-specific traits of biological systems. To overcome this limitation, we proposed the concept of a "spatiotemporal network motif," a spatiotemporal sequence of network motifs of sub-networks which are active only at specific time points and body parts.
resultsOn the basis of this concept, we analyzed the developmental gene regulatory network of the Drosophila melanogaster embryo. We identified spatiotemporal network motifs and investigated their distribution pattern in time and space. As a result, we found how key developmental processes are temporally and spatially regulated by the gene network. In particular, we found that nested feedback loops appeared frequently throughout the entire developmental process. From mathematical simulations, we found that mutual inhibition in the nested feedback loops contributes to the formation of spatial expression patterns.
conclusionsTaken together, the proposed concept and the simulations can be used to unravel the design principle of developmental gene regulatory networks.
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