Description

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

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.

Reuse Permissions
  • Downloads
    PDF (2.9 MB)

    Details

    Title
    • A Bag-of-Words Approach for Drosophila Gene Expression Pattern Annotation
    Date Created
    2009-04-21
    Resource Type
  • Text
  • Collections this item is in
    Identifier
    • Digital object identifier: 10.1186/1471-2105-10-119
    • Identifier Type
      International standard serial number
      Identifier Value
      1471-2105
    Note
    • The electronic version of this article is the complete one and can be found online at: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-119

    Citation and reuse

    Cite this item

    This is a suggested citation. Consult the appropriate style guide for specific citation guidelines.

    Ji, S., Li, Y., Zhou, Z., Kumar, S., & Ye, J. (2009). A bag-of-words approach for Drosophila gene expression pattern annotation. BMC Bioinformatics, 10(1), 119. doi:10.1186/1471-2105-10-119

    Machine-readable links