A Computational Approach towards a Gene Regulatory Network for the Developing Nematostella vectensis Gut
| Autor: | Daniel Botman, Eric Röttinger, Jaap A. Kaandorp, Johann de Jong, Mark Q. Martindale |
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| Přispěvatelé: | Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), The Whitney Laboratory for Marine Bioscience [St. Augustine, FL, USA], University of Florida [Gainesville] (UF), Section Computational Science, University of Amsterdam [Amsterdam] (UvA), Computational Science Lab (IVI, FNWI) |
| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
Computer and Information Sciences
food.ingredient Organogenesis Gene regulatory network Gene Expression Embryonic Development lcsh:Medicine Nematostella Genetic Networks Computational biology Bioinformatics food Gene expression Morphogenesis Genetics medicine Animals Cluster Analysis Gene Regulatory Networks Pattern Formation lcsh:Science Gene [SDV.BDD]Life Sciences [q-bio]/Development Biology Regulatory Networks Regulation of gene expression Multidisciplinary biology Systems Biology Gene Expression Profiling lcsh:R Biology and Life Sciences Computational Biology Gene Expression Regulation Developmental Starlet sea anemone Body Plan Organization biology.organism_classification Gastrointestinal Tract Gene expression profiling Sea Anemones medicine.anatomical_structure lcsh:Q Endoderm Network Analysis Research Article Developmental Biology |
| Zdroj: | PLoS ONE PLoS ONE, Public Library of Science, 2014, 9 (7), pp.e103341. ⟨10.1371/journal.pone.0103341⟩ PLoS ONE, Vol 9, Iss 7, p e103341 (2014) PLoS ONE, 9(7):e103341. Public Library of Science |
| ISSN: | 1932-6203 |
| DOI: | 10.1371/journal.pone.0103341⟩ |
| Popis: | BackgroundThe starlet sea anemone Nematostella vectensis is a diploblastic cnidarian that expresses a set of conserved genes for gut formation during its early development. During the last decade, the spatial distribution of many of these genes has been visualized with RNA hybridization or protein immunolocalization techniques. However, due to N. vectensis' curved and changing morphology, quantification of these spatial data is problematic. A method is developed for two-dimensional gene expression quantification, which enables a numerical analysis and dynamic modeling of these spatial patterns.Methods/ResultIn this work, first standardized gene expression profiles are generated from publicly available N. vectensis embryo images that display mRNA and/or protein distributions. Then, genes expressed during gut formation are clustered based on their expression profiles, and further grouped based on temporal appearance of their gene products in embryonic development. Representative expression profiles are manually selected from these clusters, and used as input for a simulation-based optimization scheme. This scheme iteratively fits simulated profiles to the selected profiles, leading to an optimized estimation of the model parameters. Finally, a preliminary gene regulatory network is derived from the optimized model parameters.OutlookWhile the focus of this study is N. vectensis, the approach outlined here is suitable for inferring gene regulatory networks in the embryonic development of any animal, thus allowing to comparatively study gene regulation of gut formation in silico across various species. |
| Databáze: | OpenAIRE |
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