Bioinformatics beyond sequence: Mapping gene function in the embryo

Nature Reviews Genetics

Volumn 2, Issue 6, 2001, Pages 409-417

  Davidson, Duncan ^a   Baldock, Richard ^a  

^a WESTERN GENERAL HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; BIOLOGY; EMBRYO; GENE EXPRESSION REGULATION; HUMAN; METABOLISM; MUTATION; REVIEW;

ANIMALS; COMPUTATIONAL BIOLOGY; EMBRYO; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HUMANS; MUTATION;

EID: 0035380760     PISSN: 14710056     EISSN: None     Source Type: Journal    
DOI: 10.1038/35076500     Document Type: Review

References (45)

1. Nadeau, J. H. Muta-genetics of muta-genomics: the feasibility of large-scale mutagenesis and phenotyping programs. Mamm. Genome 11, 603-607 (2000). A thoughtful and provocative discussion of systematic approaches to capturing gene function data at the organism level.
2. Paigen, K. & Eppig, J. T. A mouse phenome project. Mamm. Genome 11, 715-717 (2000).
3. Bray, D. Reductionism for biochemists: how to survive the protein jungle. Trends Biochem. Sci. 22, 325-326 (1997).
4. Achard, F., Vaysseix, G. & Barillot, E. XML, bioinformatics and data integration. Bioinformatics 17, 115-125 (2001).
5. The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genet. 25, 25-29 (2000). Gene Ontology is an excellent example of a dynamic bioinformatic framework that aims to unify our understanding of gene function across species and different levels of biological organization.
6. Streicher, J. et al. Computer-based three-dimensional visualization of developmental gene expression. Nature Genet. 25, 147-152 (2000).
7. Hecksher-Sorensen, J. & Sharpe, J. 3D confocal reconstruction of gene expression in mouse. Mech. Dev. 100, 59-63 (2001).
8. Ringwald, M., Eppig, J. T., Kadin, J. A., Richardson, J. E. & the Gene Expression Database Group. GXD: a gene expression database for the laboratory mouse: current status and recent enhancements. Nucleic Acids Res. 28, 115-119 (2000).
9. Lester, H. & Arridge, S. R. A survey of hierarchical non-linear medical image registration. Pattern Recognition 32, 129-149 (1999).
10. Toga, A. W. & Thompson, P. M. The role of image registration in brain mapping. Image Vision Comput. 19, 3-24 (2001).
11. Baldock, R., Bard, J., Kaufman, M. H. & Davidson, D. A real mouse for your computer. BioEssays 14, 501-502 (1992).
12. Brune, R. M. et al. A three-dimensional model of the mouse at embryonic day 9. Dev. Biol. 216, 457-468 (1999).
13. Bard, J. et al. An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature. Mech. Dev. 74, 111-120 (1998).
14. Theiler, K. The House Mouse. Atlas of Embryonic Development (Springer, New York, 1989).
15. Kaufman, M. H. The Atlas of Mouse Development (Academic, London, 1992).
16. Davidson, D., Bard, J., Kaufman, M. H. & Baldock, R. The Mouse Atlas Database: a community resource for mouse development. Trends Genet. 17, 49-51 (2001).
17. Louie, A. Y. et al. In vivo visualization of gene expression using magnetic resonance imaging. Nature Biotechnol. 18, 321-325 (2000).
18. Verbeek, F. J. et al. A standard atlas of zebrafish development for projection of experimental data. Proc. Int. Soc. Opt. Engng 3964, 242-252 (2000).
19. Hartenstein, V., Lee, A. & Toga, A. W. A graphical digital database of Drosophila embryogenesis. Trends Genet. 11, 51-58 (1995). An excellent discussion of the issues involved in building an atlas database framework for Drosophila.
20. Toga, A. W. Brain Warping (Academic, San Diego, 1999). A collection of authoritative papers on methods to combine and compare three-dimensional images of mammalian brains.
21. Toga, A. W. & Thompson, P. in Brain Warping (ed. Toga, A. W.) 1-26 (Academic, San Diego, 1999).
22. Toga, A. W., Santori, E. M., Hazani, R. & Ambach, K. A digital map of rat brain. Brain Res. Bull. 38, 77-85 (1995).
23. Raff, R. A. Evo-devo: the evolution of a new discipline. Nature Rev. Genet 1, 74-79 (2000).
24. Davidson, D. et al. in In situ Hybridization, a Practical Approach (ed. Wilkinson, D.) 190-214 (IRL, Oxford, 1998).
25. Drysdale, R. Phenotypic data in FlyBase. Briefings Bioinform. 2, 68-80 (2001). A good, practical description of how FlyBase addresses the problems of describing mutant phenotype in a bioinformatic context.
26. Eppig, J. T. Algorithms for mutant sorting. Mamm. Genome 11, 584-589 (2001). A discussion of work to incorporate phenotypic descriptors into the textual bioinformatics framework for the mouse. Compare with reference 25.
27. Ringwald, M. et al. A database for mouse development. Science 265, 2033-2034 (1994).
28. Allen, J. F. Maintaining knowledge about temporal intervals. Commun. Assoc. Comput. Machin. 26, 832-843 (1983).
29. Vidal, M. A biological atlas of functional maps. Cell 104, 333-339 (2001).
30. van Helden, J. et al. Biological function from the network of molecules and interactions. Briefings Bioinform. 2, 81-93 (2001).
31. Karp, P. D. An ontology for biological function based on molecular interactions. Bioinformatics 16, 269-285 (2000).
32. Rzhetsky, A. et al. A knowledge model for analysis and simulation of regulatory networks. Bioinformatics 16, 1120-1128 (2000).
33. Hillis, D. M. & Holder, M. T. in New Technologies for Life Sciences: a Trends Guide (ed. Wood, R.) 47-50 (Elsevier Science, London, 2000).
34. Tomita, M. et al. E-CELL: software environment for whole-cell simulation. Bioinfomatics 15, 72-84 (1999).
35. von Dassow, G., Meir, E., Munro, E. & Odell, G. M. The segment polarity network is a robust developmental module. Nature 406, 188-192 (2000).
36. The FlyBase Consortium. The FlyBase Database of the Drosophila Genome Projects and community literature. Nucleic Acids Res. 27, 85-88 (1999).
37. Stein, L., Sternberg, P., Durbin, R., Theirry-Mieg, J. & Spieth, J. WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res. 29, 82-86 (2001).
38. Sulston, J. E., Scherienberg, E., White, J. G. & Thomson, J. N. The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100, 64-119 (1983).
39. Campos-Ortega, J. A. & Hartenstein, V. The Embryonic Development of Drosophila melanogaster (Springer, Berlin, 1985).
40. Nieuwkoop, P. D. & Faber, J. Normal Table of Xenopus laevis (North Holland, Amsterdam, 1967).
41. Kimmel, C. B., Ballard, W. W., Kimmel, S. R., Ullmann, B. & Schilling, T. F. Stages of embryonic development of the zebrafish. Dev. Dynamics 203, 253-310 (1995).
42. Hamburger, V. & Hamilton, H. L. A series of normal stages in the development of the chick embryo. J. Morphol. 88, 49-93 (1951).
43. Downes, K. M. & Davies, T. Staging of gastrulating mouse embryos by morphological landmarks in the dissecting microscope. Development 118, 1255-1266 (1993).
44. O'Rahilly, R. & Muller, F. Developmental Stages In Human Embryos Including a Revision of Streeter's 'Horizons' and a Survey of the Carnegie Collection (Carnegie Institute, Washington DC, 1987).
45. Anonymous. Nomina Anatomica, Nomina Histologica, Nomina Embryologica (Churchill Livingston, Edinburgh, 1992).