4DXpress:: a database for cross-species expression pattern comparisons
4DXpress:: a database for cross-species expression pattern comparisons
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DOI：
10.1093/nar/gkm797
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发表时间：
2008-01-01
影响因子：
14.9
通讯作者：
Henrich, Thorsten
中科院分区：
文献类型：
--
作者：
Haudry, Yannick;Berube, Hugo;Henrich, Thorsten
在小鼠、鱼类或果蝇等主要动物模型物种中，通过整体原位杂交实验可以获取基因随时间变化的详细空间信息。在这些物种中，许多基因的表达模式已经得到研究，并且数据已整合到专门的模式生物数据库中，例如斑马鱼的ZFIN、青鳉的MEPD、果蝇的BDGP或小鼠的GXD。然而，一个允许用户查询和比较不同物种基因表达模式的中心存储库尚未建立。因此，我们已经将斑马鱼、果蝇、青鳉和小鼠的表达模式整合到一个名为4DXpress（四维表达数据库）的中心公共存储库中。用户可以跨物种查询基于解剖学术语的表达注释，并快速从一个基因跳转到其他物种中的同源基因。基因与ArrayExpress中的公共微阵列数据相关联。我们已经绘制了物种之间的发育阶段图谱，以便能够比较发育时间阶段。我们在一个单独的资源中存储了迄今为止数量最多的基因表达模式集合，涵盖了16505个已注释基因。4DXpress对于发育生物学家以及对基因调控和进化感兴趣的计算生物学家来说将是一个非常宝贵的工具。4DXpress可在……获取。
In the major animal model species like mouse, fish or fly, detailed spatial information on gene expression over time can be acquired through whole mount in situ hybridization experiments. In these species, expression patterns of many genes have been studied and data has been integrated into dedicated model organism databases like ZFIN for zebrafish, MEPD for medaka, BDGP for Drosophila or GXD for mouse. However, a central repository that allows users to query and compare gene expression patterns across different species has not yet been established. Therefore, we have integrated expression patterns for zebrafish, Drosophila, medaka and mouse into a central public repository called 4DXpress (expression database in four dimensions). Users can query anatomy ontology-based expression annotations across species and quickly jump from one gene to the orthologues in other species. Genes are linked to public microarray data in ArrayExpress. We have mapped developmental stages between the species to be able to compare developmental time phases. We store the largest collection of gene expression patterns available to date in an individual resource, reflecting 16 505 annotated genes. 4DXpress will be an invaluable tool for developmental as well as for computational biologists interested in gene regulation and evolution. 4DXpress is available at