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Analysis of a spatial gene expression database for sea anemone Nematostella vectensis during early development.

Botman D, Jansson F, Röttinger E, Martindale MQ, de Jong J, Kaandorp JA - BMC Syst Biol (2015)

Bottom Line: A correlation analysis has been performed on the resulting numerical gene expression profiles for each stage.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.

View Article: PubMed Central - PubMed

Affiliation: Computational Science, University of Amsterdam, Science Park 904, Amsterdam, The Netherlands. d.botman@uva.nl.

ABSTRACT

Background: 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.

Methods: 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.

Results: 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.

Discussion: 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.

Conclusions: 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.

No MeSH data available.


Related in: MedlinePlus

Gene expression quantification pipeline. A digital morphology is overlaid with the gene expression image (a) and the points are manually dragged over the embryo’s cell layer (b). After the cell layer is decomposed into segments (c) and the intensity is plotted as a function of cell layer position (d), the profile is manually edited to correct for artifacts (e)
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Fig3: Gene expression quantification pipeline. A digital morphology is overlaid with the gene expression image (a) and the points are manually dragged over the embryo’s cell layer (b). After the cell layer is decomposed into segments (c) and the intensity is plotted as a function of cell layer position (d), the profile is manually edited to correct for artifacts (e)

Mentions: The genes listed in the Kahi Kai database for N. vectensis are screened for useful expression patterns. For one-dimensional quantification, suitable genes are genes that display cylindrical expression in broad domains up to the late planula stage. Other genes, such as those that are expressed on the syphonoglyph side only or in individual cells, require a two-dimensional or three-dimensional quantification method for a complete description. In situ hybridization images are imported into GenExp, a MATLAB interface designed to extract and quantify gene expression patterns [5]. A continuous series of digital morphologies has been derived from a confocal microscopy study on N. vectensis gastrulation. A digital morphology is selected and overlaid with the hybridization image (Fig. 3a). To get a correct alignment, the points of the digital morphology are dragged over the observed cell layer boundaries (Fig. 3b). The cell layer is divided into segments with edges between the inner and outer cell layer boundaries (Fig. 3c). The color intensities of the pixels within each segment are averaged and plotted as a function of the segment’s position on the cell layer (Fig. 3d). This plot is edited to compensate for artifacts from the environment, annotations and imperfections in the segmentation (Fig. 3e). The edited plot is interpolated at a hundred equidistant points and the intensity is scaled to unity to arrive at a standardized expression profile. The standardized profiles are ordered in seven groups from blastula to late planula, based on the development label of the source images. The profiles within each group are clustered with average linkage and Pearson correlation distance. The groups are divided into two main clusters, or into three clusters if the second split reduces the largest branch. The profiles within these main clusters are displayed in combined plots. Profiles in any apparent subclusters are plotted together as well.Fig. 3


Analysis of a spatial gene expression database for sea anemone Nematostella vectensis during early development.

Botman D, Jansson F, Röttinger E, Martindale MQ, de Jong J, Kaandorp JA - BMC Syst Biol (2015)

Gene expression quantification pipeline. A digital morphology is overlaid with the gene expression image (a) and the points are manually dragged over the embryo’s cell layer (b). After the cell layer is decomposed into segments (c) and the intensity is plotted as a function of cell layer position (d), the profile is manually edited to correct for artifacts (e)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4581490&req=5

Fig3: Gene expression quantification pipeline. A digital morphology is overlaid with the gene expression image (a) and the points are manually dragged over the embryo’s cell layer (b). After the cell layer is decomposed into segments (c) and the intensity is plotted as a function of cell layer position (d), the profile is manually edited to correct for artifacts (e)
Mentions: The genes listed in the Kahi Kai database for N. vectensis are screened for useful expression patterns. For one-dimensional quantification, suitable genes are genes that display cylindrical expression in broad domains up to the late planula stage. Other genes, such as those that are expressed on the syphonoglyph side only or in individual cells, require a two-dimensional or three-dimensional quantification method for a complete description. In situ hybridization images are imported into GenExp, a MATLAB interface designed to extract and quantify gene expression patterns [5]. A continuous series of digital morphologies has been derived from a confocal microscopy study on N. vectensis gastrulation. A digital morphology is selected and overlaid with the hybridization image (Fig. 3a). To get a correct alignment, the points of the digital morphology are dragged over the observed cell layer boundaries (Fig. 3b). The cell layer is divided into segments with edges between the inner and outer cell layer boundaries (Fig. 3c). The color intensities of the pixels within each segment are averaged and plotted as a function of the segment’s position on the cell layer (Fig. 3d). This plot is edited to compensate for artifacts from the environment, annotations and imperfections in the segmentation (Fig. 3e). The edited plot is interpolated at a hundred equidistant points and the intensity is scaled to unity to arrive at a standardized expression profile. The standardized profiles are ordered in seven groups from blastula to late planula, based on the development label of the source images. The profiles within each group are clustered with average linkage and Pearson correlation distance. The groups are divided into two main clusters, or into three clusters if the second split reduces the largest branch. The profiles within these main clusters are displayed in combined plots. Profiles in any apparent subclusters are plotted together as well.Fig. 3

Bottom Line: A correlation analysis has been performed on the resulting numerical gene expression profiles for each stage.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.

View Article: PubMed Central - PubMed

Affiliation: Computational Science, University of Amsterdam, Science Park 904, Amsterdam, The Netherlands. d.botman@uva.nl.

ABSTRACT

Background: 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.

Methods: 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.

Results: 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.

Discussion: 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.

Conclusions: 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.

No MeSH data available.


Related in: MedlinePlus