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    A bag-of-words approach for Drosophila gene expression pattern annotation

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    A bag-of-words approach for ...
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    Genre
    Journal Article
    Date
    2009-04-21
    Author
    Ji, S
    Li, YX
    Zhou, ZH
    Kumar, S
    Ye, J
    Subject
    Animals
    Computational Biology
    Databases, Genetic
    Drosophila
    Gene Expression
    Gene Expression Profiling
    Pattern Recognition, Automated
    Permanent link to this record
    http://hdl.handle.net/20.500.12613/5580
    
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    DOI
    10.1186/1471-2105-10-119
    Abstract
    Background: Drosophila gene expression pattern images document the spatiotemporal dynamics of gene expression during embryogenesis. A comparative analysis of these images could provide a fundamentally important way for studying the regulatory networks governing development. To facilitate pattern comparison and searching, groups of images in the Berkeley Drosophila Genome Project (BDGP) high-throughput study were annotated with a variable number of anatomical terms manually using a controlled vocabulary. Considering that the number of available images is rapidly increasing, it is imperative to design computational methods to automate this task. Results: We present a computational method to annotate gene expression pattern images automatically. The proposed method uses the bag-of-words scheme to utilize the existing information on pattern annotation and annotates images using a model that exploits correlations among terms. The proposed method can annotate images individually or in groups (e.g., according to the developmental stage). In addition, the proposed method can integrate information from different two-dimensional views of embryos. Results on embryonic patterns from BDGP data demonstrate that our method significantly outperforms other methods. Conclusion: The proposed bag-of-words scheme is effective in representing a set of annotations assigned to a group of images, and the model employed to annotate images successfully captures the correlations among different controlled vocabulary terms. The integration of existing annotation information from multiple embryonic views improves annotation performance. © 2009 Ji et al; licensee BioMed Central Ltd.
    Citation to related work
    Springer Science and Business Media LLC
    Has part
    BMC Bioinformatics
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    ae974a485f413a2113503eed53cd6c53
    http://dx.doi.org/10.34944/dspace/5562
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