Mapping Gene Function in the Embryo

Abstract

Diverse information relating to gene function in the embryo such as gene expression and mutant phenotype can be integrated by mapping data from individual experiments to the appropriate location in a canonical digital model of the embryo. This information is then accessible to bioinformatics and can be collated, searched and compared. The development of canonical model embryos and of tools to map data to them is an active area of research.

Keywords: bioinformatics; development; atlas; organism, gene expression, mouse, ontology, anatomy

Figure 1.

EMAP section browser: one of the browser interfaces for the mouse atlas framework. The left‐hand window depicts a diagram of the selected embryo stage (in this case Theiler 13), to provide feedback for the selected section view (center panel). The section view provides live feedback of the underlying anatomy, which can be selected and highlighted (blue region). When selected, the corresponding component in the anatomical nomenclature hierarchy is shown in red (right‐hand panel).

Figure 2.

Mapping gene expression from an experimental specimen to a reference model in the EMAP by warping. The specimen containing raw data is matched to a model of the corresponding stage in the atlas framework. A section plane in the model (left panel) is selected that best corresponds to the specimen (middle panel). Corresponding positions (shown as green dots, see magnified region) are identified in the two images and used to derive an image transformation that enables all positions in the specimen to be approximately mapped to the atlas model (right panel: green, model; lilac, transformed specimen image). The result can be edited to ensure that the mapped data corresponds as closely as required to the original raw data.

Figure 3.

Screen‐shot of the MAPaint program (left‐hand group) used for viewing arbitrary sections through the framework models. The planes of section are shown in shaded yellow within the 3D navigator window, which also shows the outlines of selected anatomical structures. Each of the section windows has independent controls for adjusting the section location and orientation (center window). The right‐hand window shows patterns returned from a database query: two mapped patterns compared. The comparison is between Msx2 (red) and Msx1 (homeobox Msh‐like 1; green).

close

References

Bard J, Kaufman MH, Dubreuil C, et al. (1998) An internet‐accessible database of mouse developmental anatomy based on a systematic nomenclature. Mechanisms of Development 74: 111–120.

Davidson D, Baldock R, Bard J, et al. (1998) Gene expression databases. In: Wilkinson D (ed.) In situ Hybridization, a Practical Approach, pp. 190–214. Oxford, UK: IRL Press

Davidson D, Bard J, Kaufman MH and Baldock R (2001) The Mouse Atlas Database: a community resource for mouse development. Trends in Genetics 17: 49–51.

Drysdale R (2001) Phenotypic data in FlyBase. Briefings in Bioinformatics 2: 68–80.

Eppig JT (2001) Algorithms for mutant sorting. Mammalian Genome 11: 584–589.

Gene Ontology Consortium (2000) Gene ontology: tool for the unification of biology. Nature Genetics 25: 25–29.

Karp PD (2000) An ontology for biological function based on molecular interactions. Bioinformatics 16: 269–285.

Ringwald M, Eppig JT, Kadin JA and Richardson JE. (2000) Gene Expression Database Group (2000) GXD: a gene expression database for the laboratory mouse: current status and recent enhancements. Nucleic Acids Research 28: 115–119.

Further Reading

Brune RM, Bard JBL, Dubreuil C, et al. (1999) A three‐dimensional model of the mouse at embryonic day 9. Developmental Biology 216: 457–468.

Davidson D and Baldock R (2001) Bioinformatics beyond sequence: mapping gene function in the embryo. Nature Reviews Genetics 2: 409–417.

Hartenstein V, Lee A and Toga AW (1995) A graphical digital database of Drosophila embryogenesis. Trends in Genetics 11: 51–58.

Toga AW (1999) Brain Warping San Diego, CA: Academic Press.

Vidal M (2001) A biological atlas of functional maps. Cell 104: 333–339.

Vize PD (2001) Online analysis of development. BioEssays 23: 549–554.

Web Links

EMAP (Edinburgh Mouse Atlas Project). The Edinburgh Mouse Atlas Project website provides an interactive digital bioinformatics framework for mouse development and a gene expression database based on this framework. The framework can be downloaded in total or in part to support bioinformatics applications in mouse functional genomics http://genex.hgu.mrc.ac.uk/About/intro.html

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Davidson, Duncan, and Baldock, Richard(Jan 2006) Mapping Gene Function in the Embryo. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005995]