Automatic recognition and annotation of gene expression patterns of fly embryos
Automatic recognition and annotation of gene expression patterns of fly embryos
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DOI：
10.1093/bioinformatics/btl680
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发表时间：
2007-03-01
期刊：
影响因子：
5.8
通讯作者：
Peng, Hanchuan
中科院分区：
文献类型：
--
作者：
Zhou, Jie;Peng, Hanchuan
动机：通过原位mRNA杂交获得的基因表达模式提供了果蝇胚胎发生过程中不同基因的重要信息。到目前为止，这些图像的注释是通过手动为图像分配解剖学本体术语子集来完成的。这个耗时的过程在很大程度上取决于专家的一致性。结果：我们开发了一个系统来自动注释基因表达的果蝇胚胎组织。我们将此任务表述为图像模式识别问题。对于新的蝇胚图像，我们的系统回答了两个问题：(1)图像属于哪个阶段范围？(2)图像应该分配哪些注释？我们提出通过多分辨率二维小波离散变换来识别小波胚胎特征，然后进行最小冗余最大相关特征选择，从而为注释产生最优的区分特征。然后，由于每张图像可能对应多个注释，我们构建了一系列并行双类预测器来解决多目标注释问题。补充信息：完整的注释预测结果可在http://www.cs.niu.edu/similar到jzhou/papers/fruitfly和http://research.janelia.org/peng/proj/fly_embryo_annotation/上获得。在实验中使用的数据集将可要求通信作者。联系方式：jzhou@cs.niu.edu和pengh@janelia.hhmi.org。
Motivation: Gene expression patterns obtained by in situ mRNA hybridization provide important information about different genes during Drosophila embryogenesis. So far, annotations of these images are done by manually assigning a subset of anatomy ontology terms to an image. This time-consuming process depends heavily on the consistency of experts.Results: We develop a system to automatically annotate a fruitfly's embryonic tissue in which a gene has expression. We formulate the task as an image pattern recognition problem. For a new fly embryo image, our system answers two questions: ( 1) Which stage range does an image belong to? ( 2) Which annotations should be assigned to an image? We propose to identify the wavelet embryo features by multi-resolution 2D wavelet discrete transform, followed by min-redundancy max-relevance feature selection, which yields optimal distinguishing features for an annotation. We then construct a series of parallel bi-class predictors to solve the multi-objective annotation problem since each image may correspond to multiple annotations.Supplementary information: The complete annotation prediction results are available at: http://www.cs.niu.edu/similar to jzhou/papers/fruitfly and http://research.janelia.org/peng/proj/fly_embryo_annotation/. The datasets used in experiments will be available upon request to the correspondence author.Contact: jzhou@cs.niu.edu and pengh@janelia.hhmi.org.