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Analysis of a spatial gene expression database for sea anemone Nematostella vectensis during early development
Daniel Botman1, Fredrik Jansson1, Eric Röttinger2,3,4, Mark Q. Martindale5, Johann de Jong6 and Jaap A. Kaandorp1
1 Computational Science, University of Amsterdam, Science Park 904, Amsterdam, The Netherlands
2 Université Nice Sophia Antipolis, Institute for Research on Cancer and Aging, Nice (IRCAN), UMR 7284, Nice, France
3 Centre National de la Recherche Scientifique (CNRS), Institute for Research on Cancer and Aging, Nice (IRCAN), UMR 7284, Nice, France
4 Institut National de la Santé et de la Recherche Médicale (INSERM), Institute for Research on Cancer and Aging, Nice (IRCAN), U1081, Nice, France
5 Whitney Lab for Marine Bioscience, University of Florida, St. Augustine, FL, USA
6 Computational Cancer Biology Group, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
BMC Systems Biology 2015, 9:63.
The spatial distribution of many genes has been visualized during the embryonic development in the starlet sea anemone Nematostella vectensis in the last decade. In situ hybridization images are available in the Kahi Kai gene expression database, and a method has been developed to quantify spatial gene expression patterns of N. vectensis. In this paper, gene expression quantification is performed on a wide range of gene expression patterns from this database and descriptions of observed expression domains are stored in a separate database for further analysis.
Spatial gene expression from suitable in situ hybridization images has been quantified with the GenExp program. A correlation analysis has been performed on the resulting numerical gene expression profiles for each stage. Based on the correlated clusters of spatial gene expression and detailed descriptions of gene expression domains, various mechanisms for developmental gene expression are proposed.
In the blastula and gastrula stages of development in N. vectensis, its continuous sheet of cells is partitioned into correlating gene expression domains. During progressing development, these regions likely correspond to different fates. A statistical analysis shows that genes generally remain expressed during the planula stages in those major regions that they occupy at the end of gastrulation.
Observed shifts in gene expression domain boundaries suggest that elongation in the planula stage mainly occurs in the vegetal ring under the influence of the gene Rx. The secondary body axis in N. vectensis is proposed to be determined at the mid blastula transition.
Early gene expression domains in N. vectensis appear to maintain a positional order along the primary body axis. Early determination in N. vectensis occurs in two stages: expression in broad circles and rings in the blastula is consolidated during gastrulation, and more complex expression patterns appear in the planula within these broad regions. Quantification and comparison of gene expression patterns across a database can generate hypotheses about collective cell movements before these movements are measured directly.
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