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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

Hierarchical clustering of gene expression profiles in the early planula stage. The dendrogram is cut off at a similarity of 0.9
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Fig10: Hierarchical clustering of gene expression profiles in the early planula stage. The dendrogram is cut off at a similarity of 0.9

Mentions: For all seven stages of development from blastula to late planula, in situs of suitable genes have been quantified. The expression profiles are provided in Additional file 1 in MATLAB format. The quantified patterns are ordered in dendrograms and correlation matrices. The number of analyzed patterns from each stage are: 112 from the blastula (Fig. 6); 52 from the early gastrula (Fig. 7); 18 from the mid gastrula (Fig. 8); 25 from the late gastrula (Fig. 9); 15 from the early planula (Fig. 10); 17 from the planula (Fig. 11) and 13 from the late planula (Fig. 12). From the correlation matrices, major and minor blocks are identified. The profiles in these blocks are combined in separate plots for the blastula (Fig. 13), early gastrula (Fig. 14), mid gastrula (Fig. 15), late gastrula (Fig. 16), early planula (Fig. 17), planula (Fig. 18) and late planula (Fig. 19) stages. Correlating expression domains from the blastula to the late gastrula stages are summarized in Fig. 20.Fig. 6


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)

Hierarchical clustering of gene expression profiles in the early planula stage. The dendrogram is cut off at a similarity of 0.9
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig10: Hierarchical clustering of gene expression profiles in the early planula stage. The dendrogram is cut off at a similarity of 0.9
Mentions: For all seven stages of development from blastula to late planula, in situs of suitable genes have been quantified. The expression profiles are provided in Additional file 1 in MATLAB format. The quantified patterns are ordered in dendrograms and correlation matrices. The number of analyzed patterns from each stage are: 112 from the blastula (Fig. 6); 52 from the early gastrula (Fig. 7); 18 from the mid gastrula (Fig. 8); 25 from the late gastrula (Fig. 9); 15 from the early planula (Fig. 10); 17 from the planula (Fig. 11) and 13 from the late planula (Fig. 12). From the correlation matrices, major and minor blocks are identified. The profiles in these blocks are combined in separate plots for the blastula (Fig. 13), early gastrula (Fig. 14), mid gastrula (Fig. 15), late gastrula (Fig. 16), early planula (Fig. 17), planula (Fig. 18) and late planula (Fig. 19) stages. Correlating expression domains from the blastula to the late gastrula stages are summarized in Fig. 20.Fig. 6

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