Abstract
BackgroundThe 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.MethodsSpatial 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.ResultsIn 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.DiscussionObserved 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.ConclusionsEarly 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-015-0209-4) contains supplementary material, which is available to authorized users.
Highlights
The spatial distribution of many genes has been visualized during the embryonic development in the starlet sea anemone Nematostella vectensis in the last decade
Early gene expression domains in N. vectensis appear to maintain a positional order along the primary body axis
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
Summary
The spatial distribution of many genes has been visualized during the embryonic development in the starlet sea anemone Nematostella vectensis in the last decade. The largest potential of spatial gene product distribution datasets, is in verifying numerical models of regulatory interaction networks, which has been demonstrated for the embryonic development of fruit fly Drosophila melanogaster [3]. To perform accurate simulations of such processes, the spatial gene expression patterns need to be digitally quantified and formatted to standardized profiles. Similarity metrics are a common tool for classifying time series expression data to identify correlating dynamics among genes. These similarity measures can identify correlating spatial expression among genes from quantified expression patterns as well. To use quantified gene expression patterns in dynamic simulations, reliable time points for gene expression patterns are required
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