Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
Bioinformatics. 2011 Dec 1;27(23):3319-20. doi: 10.1093/bioinformatics/btr567. Epub 2011 Oct 12.
Images containing spatial expression patterns illuminate the roles of different genes during embryogenesis. In order to generate initial clues to regulatory interactions, biologists frequently need to know the set of genes expressed at the same time at specific locations in a developing embryo, as well as related research publications. However, text-based mining of image annotations and research articles cannot produce all relevant results, because the primary data are images that exist as graphical objects. We have developed a unique knowledge base (FlyExpress) to facilitate visual mining of images from Drosophila melanogaster embryogenesis. By clicking on specific locations in pictures of fly embryos from different stages of development and different visual projections, users can produce a list of genes and publications instantly. In FlyExpress, each queryable embryo picture is a heat-map that captures the expression patterns of more than 4500 genes and more than 2600 published articles. In addition, one can view spatial patterns for particular genes over time as well as find other genes with similar expression patterns at a given developmental stage. Therefore, FlyExpress is a unique tool for mining spatiotemporal expression patterns in a format readily accessible to the scientific community.
包含空间表达模式的图像阐明了不同基因在胚胎发生过程中的作用。为了生成对调控相互作用的初步线索，生物学家通常需要知道在发育胚胎的特定位置同时表达的基因集，以及相关的研究出版物。然而，基于文本的图像注释和研究文章挖掘无法产生所有相关结果，因为主要数据是作为图形对象存在的图像。我们开发了一个独特的知识库（FlyExpress），以方便从黑腹果蝇胚胎发生中挖掘图像。通过点击发育中不同阶段和不同视觉投影的果蝇胚胎的特定位置，用户可以立即生成基因和出版物列表。在 FlyExpress 中，每个可查询的胚胎图片都是一个热图，捕获了 4500 多个基因和 2600 多篇已发表文章的表达模式。此外，人们还可以随着时间查看特定基因的空间模式，并在给定的发育阶段找到具有相似表达模式的其他基因。因此，FlyExpress 是一种独特的工具，可用于挖掘科学界易于访问的时空表达模式。
