Heart Failure Research Center, Department of Anatomy and Embryology, Academic Medical Center, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.
Nucleic Acids Res. 2009 Dec;37(22):7349-59. doi: 10.1093/nar/gkp819.
To unravel regulatory networks of genes functioning during embryonic development, information on in situ gene expression is required. Enormous amounts of such data are available in literature, where each paper reports on a limited number of genes and developmental stages. The best way to make these data accessible is via spatio-temporal gene expression atlases. Eleven atlases, describing developing vertebrates and covering at least 100 genes, were reviewed. This review focuses on: (i) the used anatomical framework, (ii) the handling of input data and (iii) the retrieval of information. Our aim is to provide insights into both the possibilities of the atlases, as well as to describe what more than a decade of developmental gene expression atlases can teach us about the requirements of the design of the 'ideal atlas'. This review shows that most ingredients needed to develop the ideal atlas are already applied to some extent in at least one of the discussed atlases. A review of these atlases shows that the ideal atlas should be based on a spatial framework, i.e. a series of 3D reference models, which is anatomically annotated using an ontology with sufficient resolution, both for relations as well as for anatomical terms.
为了揭示胚胎发育过程中基因作用的调控网络，需要获得有关原位基因表达的信息。大量这样的数据可在文献中获得，其中每篇论文都仅报道了有限数量的基因和发育阶段。使这些数据可访问的最佳方法是通过时空基因表达图谱。本文回顾了 11 个描述脊椎动物发育并至少涵盖 100 个基因的图谱。本文重点介绍：（i）使用的解剖学框架，（ii）输入数据的处理以及（iii）信息检索。我们的目的是深入了解图谱的可能性，并描述十多年的发育基因表达图谱能为“理想图谱”的设计要求提供哪些信息。本文综述表明，在至少一个讨论的图谱中，已经在某种程度上应用了开发理想图谱所需的大多数成分。对这些图谱的回顾表明，理想的图谱应该基于空间框架，即一系列 3D 参考模型，这些模型使用具有足够分辨率的本体进行解剖学注释，无论是关系还是解剖学术语。
