Bioinformatics Advance Access originally published online on January 19, 2007
Bioinformatics 2007 23(5):589-596; doi:10.1093/bioinformatics/btl680
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Automatic recognition and annotation of gene expression patterns of fly embryos
1Department of Computer Science, Northern Illinois University, DeKalb, IL 60115 and 2Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 200147, USA
*To whom correspondence should be addressed.
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Abstract |
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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/~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{at}cs.niu.edu and pengh{at}janelia.hhmi.org
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
Received on October 3, 2006; revised on December 10, 2006; accepted on January 5, 2007
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