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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

Workflow overview. The information stored in the Kahi Kai gene expression database has been processed into convenient formats for two partly overlapping sets of genes. These processing methods and the methods used for additional analyses are described in the text. While this workflow may seem to converge to a single final result, all intermediate results can be explored for multiple purposes
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Fig2: Workflow overview. The information stored in the Kahi Kai gene expression database has been processed into convenient formats for two partly overlapping sets of genes. These processing methods and the methods used for additional analyses are described in the text. While this workflow may seem to converge to a single final result, all intermediate results can be explored for multiple purposes

Mentions: The order of application for the described methods is displayed in the diagram in Fig. 2. Note that the intermediate results provide new information on their own and can be subjected to additional analyses.Fig. 2


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)

Workflow overview. The information stored in the Kahi Kai gene expression database has been processed into convenient formats for two partly overlapping sets of genes. These processing methods and the methods used for additional analyses are described in the text. While this workflow may seem to converge to a single final result, all intermediate results can be explored for multiple purposes
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Workflow overview. The information stored in the Kahi Kai gene expression database has been processed into convenient formats for two partly overlapping sets of genes. These processing methods and the methods used for additional analyses are described in the text. While this workflow may seem to converge to a single final result, all intermediate results can be explored for multiple purposes
Mentions: The order of application for the described methods is displayed in the diagram in Fig. 2. Note that the intermediate results provide new information on their own and can be subjected to additional analyses.Fig. 2

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