Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression.
Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression.
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DOI：
10.1093/bioinformatics/btt648
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发表时间：
2014-01-15
期刊：
影响因子：
--
通讯作者：
Ye J
中科院分区：
文献类型：
--
作者：
Yuan L;Pan C;Ji S;McCutchan M;Zhou ZH;Newfeld SJ;Kumar S;Ye J
动机：黑腹果蝇是研究动物胚胎发育早期基因功能和相互关系的主要模式生物。今天，捕获果蝇基因表达模式的图像正在以比以往更高的吞吐量产生。基因表达的空间模式的分析是最有生物学意义的图像时，从一个类似的时间点在发展过程中进行比较。因此，关键的第一步是确定胚胎的发育阶段。这些信息也需要观察和分析随着发育时间的表达变化。目前，捕获空间表达模式的图像中的胚胎的发育阶段（时间）是手动注释的，这是时间和劳动密集型的。胚胎通常被指定为阶段范围，使发育时间过程的信息。这使得下游分析效率低下，并且对空间表达模式中的相似性和差异的生物学解释具有挑战性，特别是当使用自动化工具分析大量图像的表达模式时。结果：在这里，我们提出了一种新的计算方法来注释基因表达图像中的果蝇胚胎发育阶段。在对3724张图像的分析中，新方法在正确预测发育阶段方面显示出很高的准确性（79%）。此外，它还提供了一个阶段评分，使人们能够更精细地注释每个胚胎，以便在标准阶段界限内将它们分为早期和晚期发育阶段。包含相同基因的表达模式的所有图像的阶段评分使得能够直接查看任何基因在发育时间内的表达变化。我们表明，使用来自胚胎的图像在细化阶段生成的全基因组表达图谱更好地阐明了全球基因活动和变化，并且更细化的阶段注释提高了我们在基因之间发现表达模式匹配时更好地解释结果的能力。提供和实施：该软件包可在以下网址下载：http：//www.public.asu.edu/software/Fly-Project/。联系方式：jieping.ye @ asu.edu补充信息：补充数据可在生物信息学在线获得。
Motivation: Drosophila melanogaster is a major model organism for investigating the function and interconnection of animal genes in the earliest stages of embryogenesis. Today, images capturing Drosophila gene expression patterns are being produced at a higher throughput than ever before. The analysis of spatial patterns of gene expression is most biologically meaningful when images from a similar time point during development are compared. Thus, the critical first step is to determine the developmental stage of an embryo. This information is also needed to observe and analyze expression changes over developmental time. Currently, developmental stages (time) of embryos in images capturing spatial expression pattern are annotated manually, which is time- and labor-intensive. Embryos are often designated into stage ranges, making the information on developmental time course. This makes downstream analyses inefficient and biological interpretations of similarities and differences in spatial expression patterns challenging, particularly when using automated tools for analyzing expression patterns of large number of images. Results: Here, we present a new computational approach to annotate developmental stage for Drosophila embryos in the gene expression images. In an analysis of 3724 images, the new approach shows high accuracy in predicting the developmental stage correctly (79%). In addition, it provides a stage score that enables one to more finely annotate each embryo so that they are divided into early and late periods of development within standard stage demarcations. Stage scores for all images containing expression patterns of the same gene enable a direct way to view expression changes over developmental time for any gene. We show that the genomewide-expression-maps generated using images from embryos in refined stages illuminate global gene activities and changes much better, and more refined stage annotations improve our ability to better interpret results when expression pattern matches are discovered between genes. Availability and implementation: The software package is available for download at: http://www.public.asu.edu/∼jye02/Software/Fly-Project/. Contact: jieping.ye@asu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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影响因子：
64.5
作者：
Lecuyer, Eric;Yoshida, Hideki;Krause, Henry M.
通讯作者：
Krause, Henry M.
影响因子：
2.8
作者：
Magnin, Benoit;Mesrob, Lilia;Benali, Habib
通讯作者：
Benali, Habib
DOI：
10.1073/pnas.0408031102
发表时间：
2005-04-05
影响因子：
11.1
作者：
Levine, M;Davidson, EH
通讯作者：
Davidson, EH
使用FlyExpress Discovery平台在多基因家族中进行胚胎表达的比较显示，比时间差异更大。
影响因子：
2.5
作者：
Konikoff, Charlotte E.;Karr, Timothy L.;McCutchan, Michael;Newfeld, Stuart J.;Kumar, Sudhir
通讯作者：
Kumar, Sudhir
影响因子：
5.8
作者：
Kumar, Sudhir;Boccia, Kelly;Ye, Jieping
通讯作者：
Ye, Jieping